I recently switched a couple of my vaults to a custom mount point to make it easier to locate. One is a for my Google drive. It continues to work perfectly after the custom mount point. However, I have a local mount that works perfectly after initial setup until I logout/reboot my system. When I log back in and attempt to mount the Cryptomator vault, I get the message “Mount point /direction/to/mount/ is not a directory, not empty or doesn’t exist”. I’ve confirmed that it exists. It’s not empty and I don’t want it to be and it is a directory. Since it works fine when I first create it, I no that it works. However, I don’t know what changes. Any ideas are appreciated.
Only because something worked in the past does not mean it works in the present if the context changed.
The first time you selected the custom mount point it was an empty directory, therefore unlocking&mounting worked. But apparently the mountpoint contains now files, which prevents the vault from mounting.
To successfully unlock and mount your vault in Linux, the mount point needs to be an empty directory.
Hey infeo…thank you for the response. If that is the case, why does it work fine when I let Cryptomator choose but not when I select a manual location?
Well, because Cryptomator creates its own empty, directory somewhere in your home folder to mount the unlocked vault into. 
This directory will be deleted afterwards to not cause any issues.
If you want your custom mount point to work, do not place files inside the selected directory.
So, as long as I never put anything in my manual mount location it will work? I thought the mount location (whether you allow Cryptomator to choose or you choose your own) is where you access your unencrypted files. Am I missing something, or does the manual mounting option not work?
Ok, i think there is a misunderstanding here:
When your vault is locked, your custom mount point should be an empty directory.
When your vault is unlocked, the directory shows the content of your vault.
The mount point works like a magic portal (see also our blog post about dropbox encryption): If the vault is unlocked, the directory leads you into your vault. If the vault is locked, it leads nowhere.
As soon as you place files inside the directory while the vault is locked, the directory cannot be used anymore as a mount point because those block the “portal” to reappear.
Hey infeo. I thought we had a misunderstanding also, but we don’t. However, now that you have explained the function (I thought that’s how it works) I will go back to my op. The manual mount point will only work after I first create it. If I log out and back into my computer and then try to show my mount point within Cryptomator, I get the message “Mount point /direction/to/mount/ is not a directory, not empty or doesn’t exist”. Now that I know we are on the same page, I believe something isn’t working as expected.
What OS are you using?
Arch Linux with i3wm
New update…in addition to Cryptomator custom mount point not working for me, auto-login hasn’t been working for a while either. Another issue that I’ve been seeing lately that seemed unrelated is connection issues with my wired connection. I use Expressvpn and have been troubleshooting it as the probable cause of my connection issue. To my surprise, I disabled my wired connection and rebooted the computer. Cryptomator automatically logged in like it used to and Expressvpn connected much quicker than normal also. I haven’t tested to see if this corrects the custom mount yet, but I will tomorrow and post back.
Looks like all of the issues are related to network connection issues. Today I received a kernel update that broke my dkms. I had my wired connection disabled and due to the dkms issue, wifi no longer worked. This prevented all my crypto vaults from logging in automatically. I downgraded the kernel and everything works great. I even tested the Custom mount point and it appears to be working properly. I’ve tested everything through multiple reboots and all appears to be working well. I will mark as solved. Hopefully a kernel fix comes quickly for the dkms issue.
I’m glad to hear your problem is fixed (even though after some hassle…)
Regarding the error message of “not directory or not empty”: Could possibly be a not cleaned mount. For anyone stumbling over this, the following SO answer shows how to check if a directory is registered as a mount point: