You need to force it to run on a single core.
I had this problem before. I'd restart my computer and run MB on a dual core. It'd run on 60 FPS. Then I'll leave it on and come back a few hours later, and it'd drop to around 40 FPS. It doesn't happen if I run it on a single core. You need to do this on netplay too, or people won't like playing you. There are programs out there to automatically force programs to run on a set number of cores automatically so you don't have to Ctrl+Shift+Esc, Right Click, a, space, enter, each time (if you're running Win XP).