Vista Periodically Freezes Temporarily

For some reason, every few minutes all of my programs will stop
responding and I cannot do anything besides minimize windows and then
after about 30 seconds or so it'll correct itself. Seems to happen most
often when I'm browsing the internet, however I don't think it's the
browser as it A. Works fine on another computer running Vista and B.
Worked fine until recently.

I tried running sfc /scannow and it says there are some errors that
vista could not fix, so I'm running chkdsk right now to see if that will
help. Occassionally when I'm starting up there will be a message saying
that some system files are corrupt, but booting off of the vista disc
and running repair doesn't seem to fix this and I can still log in to my
desktop and do things.

Clearly something is corrupt but I have no idea how to fix it, I would
like to avoid running system restore if at all possible however as this
problem seems to just come back when I try to fix it. ( I did a clean
install of Vista last night and still, everything worked fine until I
installed Bittorrent... but bittorrent works fine on my other computer
so I don't understand what's causing it)