This was strange because I had the same problem on q3 too. But when I toggled that setting it fixed both OA and q3 although I only channged the setting in OA. Maybe there is some explanation for this, but I cant think of a good one
One thing I do get now, is the issue with the gamma going low after when you minimise the screen. When I toggle back to full screen the gamma range seems stuck between 0.1 and 1.. if I set it to 1.1 nothing happens. But if I change r_overbrightbits to 0 it changes to brighter, like my normal display.
I can get 125 with all settings high, but still varies a little on some maps. Have you tried reinstalling drivers and starting oa up with a fresh config? With 40 fps it definately sounds something is wrong rather than a few cvars thats causing such a poor performance. Hope you manage to fix it as I know what it's like. When it went to 30 fps I felt like I had travel sickness when I seemed to jump all over the place