Well that's because 1280x1024 carries a slightly different aspect ratio. This is "solved" in the Team Arena UI code (that is obviously not used yet since no .menus are produced right now)
Ah, so that would explain it.
For now you'll have to define a custom resolution and width if you want to use the less mis-aligning resolution 1280x960. To do this, go into the console (or in q3config.cfg) and put in:
/r_customWidth 1280
/r_customHeight 960
/r_mode -1
if you're in the ingame console, type /vid_restart to restart the renderer into the new resolution.
I'll use this if I run into any other problems. Thanks for helping me out.
I'm trying to stick with my desktop resolution to prevent a lot of resolution changes because I am using a very old CRT monitor that could probably go out at any time. I'm surprised the thing hasn't gone out on me yet.