Well, I'm using Project64 1.6, I've tried 1964, and that was even worse as it just wouldn't work right off the bat. I don't think it's my graphics card dying as I can run any other PC game or even emulator perfectly, it just seems to happen with N64 emulators. And as for the background tasks, i've turned everything off that I can, and it doesn't help. Like I said, for a little longer than 2 weeks I've been playing fine without a hitch, other than the first day I downloaded the emulator. During that first day I had the same problem. If it makes any difference I'm playing Smash Bros., and when I looked at the ROM list it did say there were some video errors, but I find it odd that it would work fine for more than two weeks and then decide to work improperly.
EDIT: Whenever I enter my settings menu, it comes up first with an error message that reads as follows:
"Failed to load Plugin:
C:\Program Files\Project64 1.6\Plugin\RiceVideo6.1.3DX9.dll"
Don't know if this has anything to do with it since I thought I got rid of RiceVideo, and I'm not using it anyway, I'm using Jabos Direct3D8 1.6. At any rate, the menu comes up after I click ok to the error.