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Well as you probably are aware, a cpu can't handle things forever.
Some programs, such as adobe photoshop, use an enormous amount of memory when in use and most midrange computers will bog down with that and even another program or two open.
It very well could be a virus, have you run a scan? Spyware scan? I can tell you how to do both if needed.
If you were to do what I ask, we could see the programs and what is using the memory.
As CSL said, going to msconfig will show what is happening during startup and it could easily be something that you installed accidentally with another program by clicking a box giving permission to do so.
I suggest trying uTorrent to see if it makes a difference. Its much smaller and runs easily behind other things.
And lastly, torrents will chew your bandwidth (amount of internets you can have sent to you) as well as bog your comp down and if you don't remove it from your sharelist, people will be getting it from you and that slows things down as well.
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