That's weird... My first thought was spyware and such, but it doesn't sound like the case. Still, if you haven't scanned for any recently, try it out. Adaware and Spybot S&D are two great, free scanners.
Once you mentioned that things sped up when you opened IE, I thought perhaps it's a power saver feature... I could be totally wrong, but I'm wondering if it's clocking your processor down when you're not doing so much. Perhaps for some reason it's not clocking it back up when it's suppose to. I can't recall if Intel's have this feature too, but if you have an AMD processor, search for a program called SpeedSwitchXP. It's really for laptops, but it'll work just fine on your machine. When you run it, set the "AC" performace to Max Performace and it should lock your processor at full speed...
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Desktop * Athlon X2 4200 | 2G RAM | 160G HD | 7600GT
Laptop1 * C2D T5550 | 3G RAM | 120G HD | Intel x3100
Laptop2 * C2D T5250 | 2G RAM | 160G HD | Intel x3100
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