I get similar symptoms, but not quite this servere.
Every 15 or 30 seconds, CPU usage spikes, and the system 'pauses' (mIRC in particular, can't type). After a moment, it goes back to normal.
See
this picture for the Task Manager CPU monitor..
P4 3.2Ghz HT, 1G Ram, Windows XP SP2.
Connected to 5 networks, 22 channels total.
Only two repeating timers running, neither of which does anything hard (loops through networks getting $network and $away status).