Arteveld: Don't know about the first one, since google only shows this thread in the results, but the second one is a flash game. Flash tends to be pretty CPU heavy [could be GPU too]. I'm on a two core 2.2GHz/7600GT CPU, and Binding of Isaac takes a massive FPS drop when there's a lot of fires on screen.
Perhaps the version of Flash that You're using is wonky, perhaps there's enough apps in the background to cause a slowdown. Try right clicking on the game and choosing a lower quality setting.
Thanks for the advice.
No Time to Explain sped up once I placed it in Windowed mode.
I'll check into Flash and see if I've got the latest update for Corril Slayer. I'm on a single core but just found it to be a bit silly that an 8 bitter like CS would trip up my PC.