Sigh, I should have guessed that Dokany is the problem here… Even thou they claim to be downward compatible, it seems this was not the case with the last major update and we just discoverd it after we updated the library shipped with Cryptomator. (not to be confused with the shipped Dokany installer (; ) Another problem is that currently we cannot update the Dokany installation in place, see here.
Regarding the two entries of Cryptomator: If you want to keep your settings, do not uninstall the old one! (see [Win 10] One issue discovered with 1.4.15 [Updated]) There is also a workaround for removing the old version without deleting all your settings.