I ran into this problem last year.  I'd use the No Machine NX Client for Linux from a Fedora Core 5 desktop to connect to a Gnome session on CentOS 4.  The login would work, but as soon as I opened any GUI application in the remote session, say Gnome Terminal, it would have the following problems:

• only open in the top left corner
  
• all of the window manager widgets were missing
• right click pop up menus wouldn't stay open long enough for me to pick anything
  
• numerous other problems as well

Eventually I figured out that the NX client doesn't work properly with Xorg's composite extension.  I had been using the composite extension in Xorg to test out some of the early 3D desktop effects.  Newer Linux distributions that have the 3D desktop effects integrated, such as Fedora Core 6, load Xorg's composite extension by default.

The fix for this problem is to disable the composite extension.  If you're running a distribution that is automatically loading the composite extension, put the following into the xorg.conf file:

Section "Extensions"
        Option      "Composite" "0"
EndSection

If you've manually added the composite extension, do the same as above to prevent it from loading.

After you make that change, restart the X server.  Usually, all you have to do is logout, which kills Xorg and restarts it.

Now when you use the NX client, your remote desktop will have a functioning window manager.  Of course, the unfortunate side effect is that you will lose the 3D desktop effects.

If you really want your eye candy, you could enable the extension when you want to use the 3D effects and turn it off when you want to use the NX client.  I suspect that's likely to be more trouble than it's worth.

Hopefully this helps someone out.