Fraps/MSI afterburner emulator FPS issue

First I'd like to note that I'm not sure whether or not this is the correct place for this, though its geared toward gaming and I'm a bit tired so...

Anyway, I started doing lets plays on youtube and took about a month long break after getting my video card. Attempting to record again I find I'm getting a ridiculously low frame rate on a GBA and N64 emulator, and I have no capture card. This is really confusing seeing as how I was recording them at full speed running off my i5 2320's integrated hd 2000, and I now have a gtx 560...

So the games run perfectly, but when I got to record the fps drops massively. I also did a test with a ps2 emulator, I can record it perfectly at 1080p with 60 frames... yet the gba emu runs at about 9 fps and isn't even 720p. I've also tested on skyrim a bit, and can manage 30-45 fps at 1080p with ultra settings.

Honestly I have no idea what could be the problem, seeing as how they all play fine, but the recording frame rate is terrible. I have also tried changing the rate at which both programs record.

And now sys specs - i5 2320 3ghz quad crore, ASUS nvidia geforce gtx 560, win7 64bit, 8gb ddr3 1333 ram