I have a very similar problem. Here are more details about my situation
and a fix for the problem:

Logging into the thin client appears to mess up my account when I then
go back and login to the server at a later time.  (Ie, using the same
user's GNOME account on both the client and the server. )

As soon as I have logged in one time on the thin client with a
particular user, from that point on, when I login using that user on the
server I don't get the welcome sound when the desktop is loading, don't
get sound from certain programs like the game tremulous, and I if I
click the upper right hand button to see the logout/turn off the
computer menu then X freezes and I must CTLR-ALT-BACKSPACE. This only
happens when I try to login with that user's account directly from the
server. (After I have already logged out of the thin client with that
user.)

I have found that by deleting the following 3 files in each user's home
directory upon login from the server everything is fine. I put this into
the beginning of the PreSession scripts for gdm. (GDM appears only to be
used when logging in directly from the server so this script is not run
when logging in from the thin client.)

sudo vi /etc/gdm/PreSession/Default

add these lines at the top:

rm /home/$USER/.asoundrc
rm /home/$USER/.asoundrc.asoundconf
rm /home/$USER/.pulse-cookie

That fixes both the sound problems not working from the server and the X
windows freezing problems at the server, so I can now login using the
same accounts on either the thin client or the server.

Hope this helps. Let me know if more information is required.

-- 
[edubuntu feisty] ltsp client and server sound problem
https://bugs.launchpad.net/bugs/101946
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