Philipp made me aware of your issue. Current versions of Boxcryptor for Mac OS X do not use the service menu anymore to integrate into the Finder context menu - instead Boxcryptor implements the new Finder Sync Extension which was introduced in OS X Yosemite.
It seems that Pathfinder does not support Finder Sync Extensions (e.g. Dropbox does not have sync icons in Pathfinder) and thus you do not see context menu entries from Boxcryptor in Pathfinder anymore.
To resolve this issue, you can manually create service menu entries for Boxcryptor by extracting the file Boxcryptor.app/Contents/Resources/BoxcryptorServices.service.tgz to ~/Library/Services. Afterwards Boxcryptor entries should be available in the services menu (To open Boxcryptor.app choose "Show package contents").