Thanks to Dave (Betpot author) for this solution! I read about 12 pages of the original betpot thread and found it:
Open the properties for PokerStars.exe and in Compatibility/Settings check Disable Desktop Composition. This turns off some of the Aero UI features while the app is running and makes BetPot work fine (for me at least) in Vista!
Another Vista tidbit. I tried like hell to keep User Account Controls enabled I really did. I tried it for about 6 months when I initially went to Vista. I know a lot about computers and about Microsoft products specifically and I figured that feature was important and it should work.
Wrong.
I highly recommend anyone who gets a Vista PC go and disable User Account Control immediately. It is the feature that causes you to need to run basically everything in admin mode. When you disable it, you're running how XP ran - everything runs in admin and you don't have to mess with it. I hate to be telling people to disable it but it just causes godawful problems. Full Tilt couldn't write hand histories because it didn't have access to \Program Files, etc etc etc. You have to install various things in admin mode and even then you may or may not be ok. Actually that last statement is wrong - you WILL have problems with UAC enable.
To disable UAC, which I really do high recommend, follow the steps here:
http://www.petri.co.il/disable_uac_in_windows_vista.htm
Once you do this the security thing will pester you because you have UAC disabled. Much easier to live with that than the problems UAC causes.