I'll bind a key to show fps and another to enable vsync - and so on and so forth. Well it works for the game, but when I relaunch MOH later the same binds I had put in before don't work anymore. What gives?

bump

Are you putting your binds into your custom.cfg file in your MOHAA/main directory? If not, you should do so. If it doesn't exist, just create it.
Or you could edit your unnamedsoldier.cfg file manually under MOHAA/main/configs, I think.

Done!

However, when I bind keys in RTCW they stick. Hmmmmm.