I'm can't think of how it would affect group enumeration, but check the
differences in the pam stacks between su and gdm if you're using gnome.

One way to test pam issues is have the user login via various methods and
see which ones have the correct groups. 

1. Have the user run 'xterm -ls.' Verify it still shows the old groups
2. Have the user 'su - username'. Does that show the additional groups?
3. Have the user ssh to localhost and login. Does that show the additional
groups?

On Wed, 29 Jun 2011, Patrick Cable wrote:

> On Wed, Jun 29, 2011 at 12:56 PM, Yves Dorfsman <[email protected]> wrote:
> > What about openning a terminal, then type:
> > xterm -ls
> >
> >
> > If that works, than the issue is gnome-terminal, not the environment.
> > If so, start a gnome-terminal, then:
> > Edit ==> ProfilePreferences ==> Title and Command ==> Run command as a
> > login shell
> 
> I have already set the gnome-terminal session as a login shell.
> Running 'xterm -ls' did not produce any different result.
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