Welcome to the Centrify Forums.
We are not x2go SMEs, but the question in order is this:
Did you make sure that any PAM directives (pluggable authentication modules) for the x2go program are up-to-date with the system? (e.g. some programs may not include "system-auth" in their PAM directives).
There should be a file under /etc/pam.d/ perhaps with the x2go name on it; if you look at the entries for SSH, login or other working programs, they have the proper directives in place.
Other areas to check are:
- Has the daemon been restarted after the configuration update?
- Has the system been restarted after the configuraiton update (if it's a long-running daemon)?
Looking at this page there's also some interesting information about the x2go auth service; it has to be set to PAM.
http://wiki.x2go.org/doku.php/x2gobroker:conf
R.P