Had something similar (but with VistaHP - though I dont think this matters) - pre SP1
Not sure if I put SP1 on it would have cured it, but didnt want to put it onto a very unstable system
Usually a problem after I had installed or uninstalled something, but then it started happening almost randomly (all scans with every known Anti-malware scanner known to man showed clean)
As it only happened on my main user a/c I began to systematically stop some progs loading at startup that only that a/c used (very tedious)...
Stopped then uninstalled SpyWare Doctor (got through googlepack) since then (touch wood) been OK
Dont know why and this may just be coincidence. The problem didnt start when I had installed
SpywareDr - and had been using it for months and all was well.
I am assuming I have added something that caused the mix of applications to be in conflict but it wasnt immediate - otherwise I could just get rid of the rogue.
Not running it stablised my system and I am afraid I had spent so many hours re-booting I had lost the will to determine the exact cause
Anyway good luck