I use Windows Defender. The issue occurred before and after the latest Windows update (last run this morning).
Following your message, I have rebooted the system, deactivated Windows Defender, started Cryptomator and tried counting files in the vault (selecting all files via Ctrl + A > right click on marked folders > properties).
The process starts but is still extremely slow. I stopped after 1 minute with only around 70 files/folders counted.
In the following, I share the part of the debug log which covers the time from enabling the debug mode to the first few folders counted.
10:56:18.392 [JavaFX Application Thread] DEBUG org.cryptomator.logging.DebugMode - Debug mode enabled
10:56:19.393 [App Scheduled Executor 02] DEBUG o.c.common.settings.SettingsProvider - Attempting to save settings to C:\Users\AA\AppData\Roaming\Cryptomator\settings.json
10:56:19.395 [App Scheduled Executor 02] INFO o.c.common.settings.SettingsProvider - Settings saved to C:\Users\AA\AppData\Roaming\Cryptomator\settings.json
10:56:19.591 [JavaFX Application Thread] INFO o.cryptomator.ui.fxapp.UpdateChecker - Current version: 1.6.17, lastest version: 1.6.17
10:56:20.434 [JavaFX Application Thread] DEBUG o.c.w.k.WindowsProtectedKeychainAccess - Attempting to load keychain from C:\Users\AA\AppData\Roaming\Cryptomator\keychain.json
10:56:20.435 [JavaFX Application Thread] INFO o.c.w.k.WindowsProtectedKeychainAccess - Unable to load existing keychain file, creating new keychain.
10:56:21.454 [JavaFX Application Thread] DEBUG o.c.common.vaults.VaultStats - stop recording stats
10:56:21.455 [JavaFX Application Thread] DEBUG o.c.ui.fxapp.FxApplicationTerminator - Disabling sudden termination
10:56:21.456 [JavaFX Application Thread] DEBUG o.c.ui.fxapp.FxApplicationWindows - Start unlock workflow for CM_online
10:56:21.467 [JavaFX Application Thread] DEBUG o.cryptomator.common.CommonsModule - Starting App Background Thread 003
10:56:22.727 [JavaFX Application Thread] TRACE o.c.u.k.m.PassphraseEntryController - UnlockController.unlock()
10:56:22.954 [App Background Thread 003] DEBUG o.c.cryptofs.common.BackupHelper - Verified backup file: G:\My Drive\CM_online\masterkey.cryptomator.B4784045.bkup
10:56:22.960 [App Background Thread 003] DEBUG o.c.cryptofs.common.BackupHelper - Verified backup file: G:\My Drive\CM_online\vault.cryptomator.65192CC9.bkup
10:56:23.002 [App Background Thread 003] DEBUG o.cryptomator.cryptofs.ReadonlyFlag - Vault opened for read and write.
10:56:23.290 [JavaFX Application Thread] INFO o.c.ui.unlock.UnlockWorkflow - Unlock of 'CM_online' succeeded.
10:56:23.291 [JavaFX Application Thread] DEBUG o.c.common.vaults.VaultStats - start recording stats
10:56:23.292 [fuseMount-0-main] TRACE o.c.frontend.fuse.ReadOnlyAdapter - statfs / (331989073920 / 490744049664)
10:56:23.295 [fuseMount-0-main] TRACE o.c.frontend.fuse.locks.LockManager - Creating ReadWriteLock for []
10:56:23.296 [fuseMount-0-main] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:23.297 [fuseMount-0-main] TRACE o.c.frontend.fuse.locks.LockManager - Creating ReadWriteLock for []
10:56:23.297 [fuseMount-0-main] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[]'
10:56:23.302 [fuseMount-0-main] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr / (lastModifiedTime: 2023-01-11T09:51:42.274Z, lastAccessTime: 2023-01-06T00:40:23.199Z, creationTime: 2023-01-06T00:01:09.374Z, isRegularFile: false, isDirectory: true, isSymbolicLink: false, isOther: false, size: 0, fileKey: null)
10:56:23.302 [fuseMount-0-main] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[]'
10:56:23.302 [fuseMount-0-main] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:23.315 [JavaFX Application Thread] DEBUG o.cryptomator.common.CommonsModule - Starting App Background Thread 004
10:56:24.040 [JavaFX Application Thread] TRACE o.c.u.unlock.UnlockSuccessController - UnlockSuccessController.revealAndClose()
10:56:24.041 [JavaFX Application Thread] DEBUG o.cryptomator.common.CommonsModule - Starting App Background Thread 005
10:56:24.136 [Thread-14] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.136 [Thread-14] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[]'
10:56:24.137 [Thread-14] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr / (lastModifiedTime: 2023-01-11T09:51:42.274Z, lastAccessTime: 2023-01-06T00:40:23.199Z, creationTime: 2023-01-06T00:01:09.374Z, isRegularFile: false, isDirectory: true, isSymbolicLink: false, isOther: false, size: 0, fileKey: null)
10:56:24.137 [Thread-14] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[]'
10:56:24.138 [Thread-14] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:24.138 [Thread-15] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.138 [Thread-15] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[]'
10:56:24.139 [Thread-15] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr / (lastModifiedTime: 2023-01-11T09:51:42.274Z, lastAccessTime: 2023-01-06T00:40:23.199Z, creationTime: 2023-01-06T00:01:09.374Z, isRegularFile: false, isDirectory: true, isSymbolicLink: false, isOther: false, size: 0, fileKey: null)
10:56:24.140 [Thread-15] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[]'
10:56:24.140 [Thread-15] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:24.146 [Thread-16] TRACE o.c.frontend.fuse.ReadOnlyAdapter - statfs / (331988951040 / 490744049664)
10:56:24.263 [Thread-17] TRACE o.c.frontend.fuse.locks.LockManager - Deleting ReadWriteLock for []
10:56:24.264 [Thread-17] TRACE o.c.frontend.fuse.locks.LockManager - Creating ReadWriteLock for []
10:56:24.264 [Thread-17] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.264 [Thread-18] TRACE o.c.frontend.fuse.locks.LockManager - Creating ReadWriteLock for [, desktop.ini]
10:56:24.264 [Thread-17] TRACE o.c.frontend.fuse.locks.LockManager - Deleting ReadWriteLock for []
10:56:24.264 [Thread-17] TRACE o.c.frontend.fuse.locks.LockManager - Creating ReadWriteLock for []
10:56:24.264 [Thread-18] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.264 [Thread-17] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[]'
10:56:24.264 [Thread-18] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[, desktop.ini]'
10:56:24.264 [Thread-18] TRACE o.c.frontend.fuse.locks.LockManager - Creating ReadWriteLock for [, desktop.ini]
10:56:24.264 [Thread-18] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[, desktop.ini]'
10:56:24.265 [Thread-17] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr / (lastModifiedTime: 2023-01-11T09:51:42.274Z, lastAccessTime: 2023-01-06T00:40:23.199Z, creationTime: 2023-01-06T00:01:09.374Z, isRegularFile: false, isDirectory: true, isSymbolicLink: false, isOther: false, size: 0, fileKey: null)
10:56:24.265 [Thread-17] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[]'
10:56:24.265 [Thread-17] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:24.266 [Thread-19] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.266 [Thread-19] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[]'
10:56:24.267 [Thread-19] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr / (lastModifiedTime: 2023-01-11T09:51:42.274Z, lastAccessTime: 2023-01-06T00:40:23.199Z, creationTime: 2023-01-06T00:01:09.374Z, isRegularFile: false, isDirectory: true, isSymbolicLink: false, isOther: false, size: 0, fileKey: null)
10:56:24.267 [Thread-19] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[]'
10:56:24.267 [Thread-19] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:24.268 [Thread-18] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[, desktop.ini]'
10:56:24.268 [Thread-18] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[, desktop.ini]'
10:56:24.268 [Thread-18] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:24.268 [Thread-20] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.268 [Thread-18] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr /desktop.ini failed, node not found
10:56:24.268 [Thread-20] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[]'
10:56:24.269 [Thread-20] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr / (lastModifiedTime: 2023-01-11T09:51:42.274Z, lastAccessTime: 2023-01-06T00:40:23.199Z, creationTime: 2023-01-06T00:01:09.374Z, isRegularFile: false, isDirectory: true, isSymbolicLink: false, isOther: false, size: 0, fileKey: null)
10:56:24.269 [Thread-20] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[]'
10:56:24.269 [Thread-20] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:24.270 [Thread-21] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.270 [Thread-21] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[]'
10:56:24.270 [Thread-21] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr / (lastModifiedTime: 2023-01-11T09:51:42.274Z, lastAccessTime: 2023-01-06T00:40:23.199Z, creationTime: 2023-01-06T00:01:09.374Z, isRegularFile: false, isDirectory: true, isSymbolicLink: false, isOther: false, size: 0, fileKey: null)
10:56:24.270 [Thread-21] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[]'
10:56:24.271 [Thread-21] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:24.271 [Thread-22] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.271 [Thread-22] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[]'
10:56:24.272 [Thread-22] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr / (lastModifiedTime: 2023-01-11T09:51:42.274Z, lastAccessTime: 2023-01-06T00:40:23.199Z, creationTime: 2023-01-06T00:01:09.374Z, isRegularFile: false, isDirectory: true, isSymbolicLink: false, isOther: false, size: 0, fileKey: null)
10:56:24.272 [Thread-22] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[]'
10:56:24.272 [Thread-22] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:24.272 [Thread-23] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.272 [Thread-23] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[]'
10:56:24.273 [Thread-23] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr / (lastModifiedTime: 2023-01-11T09:51:42.274Z, lastAccessTime: 2023-01-06T00:40:23.199Z, creationTime: 2023-01-06T00:01:09.374Z, isRegularFile: false, isDirectory: true, isSymbolicLink: false, isOther: false, size: 0, fileKey: null)
10:56:24.273 [Thread-23] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[]'
10:56:24.273 [Thread-23] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:24.279 [Thread-24] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.279 [Thread-24] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[]'
10:56:24.280 [Thread-24] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr / (lastModifiedTime: 2023-01-11T09:51:42.274Z, lastAccessTime: 2023-01-06T00:40:23.199Z, creationTime: 2023-01-06T00:01:09.374Z, isRegularFile: false, isDirectory: true, isSymbolicLink: false, isOther: false, size: 0, fileKey: null)
10:56:24.280 [Thread-24] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[]'
10:56:24.280 [Thread-24] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:24.280 [Thread-25] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.281 [Thread-25] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[]'
10:56:24.281 [Thread-25] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr / (lastModifiedTime: 2023-01-11T09:51:42.274Z, lastAccessTime: 2023-01-06T00:40:23.199Z, creationTime: 2023-01-06T00:01:09.374Z, isRegularFile: false, isDirectory: true, isSymbolicLink: false, isOther: false, size: 0, fileKey: null)
10:56:24.281 [Thread-25] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[]'
10:56:24.281 [Thread-25] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:24.285 [Thread-26] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.285 [Thread-26] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[]'
10:56:24.285 [Thread-26] TRACE o.c.frontend.fuse.ReadOnlyAdapter - readdir /
10:56:24.289 [Thread-26] TRACE o.c.c.dir.CryptoDirectoryStream - OPEN
10:56:24.316 [JavaFX Application Thread] DEBUG o.cryptomator.common.CommonsModule - Starting App Background Thread 006
10:56:24.350 [Thread-26] TRACE o.c.c.dir.CryptoDirectoryStream - CLOSE
10:56:24.351 [Thread-26] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[]'
10:56:24.351 [Thread-26] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
10:56:24.351 [Thread-28] TRACE o.c.frontend.fuse.locks.LockManager - Creating ReadWriteLock for [, Folder_A]
10:56:24.351 [Thread-28] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[]'
10:56:24.351 [Thread-28] TRACE o.c.f.fuse.locks.PathRLockImpl - Acquired read path lock for '[, Folder_A]'
10:56:24.351 [Thread-28] TRACE o.c.frontend.fuse.locks.LockManager - Creating ReadWriteLock for [, Folder_A]
10:56:24.351 [Thread-28] TRACE o.c.f.fuse.locks.DataRLockImpl - Acquired read data lock for '[, Folder_A]'
10:56:24.355 [Thread-28] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr /Folder_A (lastModifiedTime: 2023-01-09T21:47:56.601Z, lastAccessTime: 2023-01-09T21:47:01.313Z, creationTime: 2023-01-09T21:47:01.313Z, isRegularFile: false, isDirectory: true, isSymbolicLink: false, isOther: false, size: 0, fileKey: null)
10:56:24.355 [Thread-28] TRACE o.c.f.fuse.locks.DataRLockImpl - Released read data lock for '[, Folder_A]'
10:56:24.355 [Thread-28] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[, Folder_A]'
10:56:24.355 [Thread-28] TRACE o.c.f.fuse.locks.PathRLockImpl - Released read path lock for '[]'
I’m not familiar with analyzing such log files and did not find anything unusual except for this node not found item:
10:56:24.268 [Thread-18] TRACE o.c.frontend.fuse.ReadOnlyAdapter - getattr /desktop.ini failed, node not found