One of the first things you need to do when setting up a linux workstation for use with Houdini is to alter the windows functions so you can alt-left click to set keyframes(and as you mention, some navigation issues). I use KDE myself, so I'm afraid I can't help you with the specifics on Gnome, assuming you're using that flavour of Ubuntu. In KDE it's under Desktop/Window Behavior/Window Actions and set the modifier key + left button to do nothing rather than move windows around.
Used to be for the longest time Gnome didn't allow you to change that(see: Metacity and Pennington, Havoc) but from what I've heard you can do that now. A quick google found this, which should send you in the right direction, something to do with the third level chooser, whatever that is:
http://www.computerworld.com.au/index.php/id;1140961447;fp;2;fpid;37;pf;1 [computerworld.com.au]
If that's not it, you basically want to wring control of your alt key back from metacity, in terms of what to search for.
Cheers,
J.C.