Same problem here. Version 1.5.6, 64 bit, Windows 10, Dokany.
Uninstalled and reinstalled Cryptomator and Dokany several times, rebooting after each step. Deleted dokan1.dll from Windows\system32 and from Progams\Cryptomator. Also updated Dokay and made sure that correct versions showed up in the log file for Dokany (140) and Dokany driver (400). Also tried using the CURRENT_SESSION flag.
Still the same behaviour. After reboot Cryptomator starts and volume is mounted and accessible, but after 1-2 minutes it is gone. This also happens while copying or having files opened.
Now gone back to version 1.4.12. This was the last version without automount problems, at least for me. Troubles started with 1.4.15 latest, as far as I can tell.
Sorry for my english, I’m not a native speaker. It’s also my first post, so comments on what to improve are welcome.