Ok, an update and a clarification:
I downloaded and installed the official ATI drivers for my Radeon 9600XT. Those seem to have installed correctly and I have access to the ATI Catalyst Control Center and all the card options.
Then I re-ran the 'Start Media Center' link that was installed into the "applications"->"sound and Video" -> "start Media Center" menu item in Ubantu. It ran through it's setup script and the things that I noticed are below:
1. THe pluto ATI drivers for my card were not installed because they could not be downloaded by the script.
2. The HALd (hardware abstraction layer daemon) was not started and could not be started. Don't know the implications of this problem on the video subsystem.
3. When it changed vid modes it threw a popup that said "Orbiter failed to setup the transparency, please check if the transparency manager is running"
From that point I could only acknowledge the popup then it would eventually come back. I couldn't get past this point.
I understand that with the Radeon vid cards you have to use 'masking' and disable 'alpha blending' but I don't know how to do that? Any suggestions of 1) how to disable alpha blending 2) enable masking, and 3) if that would get rid of this Orbiter popup?