By default, the Boxcryptor Drive is only available to the current user. Some backup software is actually run as a different user (e.g. system service) and thus can't see the Boxcryptor Drive. If you want the Boxcryptor Drive to be seen by all users on your machine, you can enable the advanced setting "Mount for all users".
More information: https://support.boxcryptor.com/display/BCWINEN/8.+Change+the+advanced+settings