I am using the restricted video driver 185 for Nvidia. Running Koala 9.10. I hooked up my TV to the S-Video output on my Nvidia 8800 GT. Everything seemed to work fine got my video to run, then I maximized and watched the show, but my desktop is larger than the screen, so my window controls (maximize, minimize, close) are out of site. I had no way to close my video after watching, beside right clicking on the task in the panel. But even then I tried reopening it and it still went to the TV screen full screen. I used the Nvidia config tool to disable the TV, and the apps still open off screen where they would if the TV was still enabled. Even other programs opened offscreen. The only thing that fixed it was logging out of X and logging back in. Now, how do I fix the screen size to match my desktop size, and how do I make it so that the programs don't remember where the TV used to be after the TV is disabled?

Have you changed the System - Preferences - Appearance - Visual Effects?

Also, have a look at:

http://sourceforge.net/projects/nv-tv-out/

NV-TV-Out is a small utility to control NVidia TV output.