| Definitely seems like your registry is corrupted, system recovery won't always correct this. Cleaning out spyware usually entails removing entries from the registry, and anti-spyware has been known to mis-identify legitimate entries as mal or spy ware. I suspect going by what you've written that this is the case with you. What anti-spyware were you using by the way, when it happened to me I was using Spy Stormer, needless to say I've never used it since.
Do you still have the original installation discs? If so, and you can't find any other solution the last resort is to wipe the drive and do a complete new re-install. I wouldn't do that just yet though, someone else might be able to offer a better solution. If it comes to the worst, back up all the data you have onto CD's, keeping a list of the relevant directories and folders that they came from so that you can put the data back in the correct place.
I hope you, or someone else can find a less traumatic solution, having had to do the above myself I know it's a real pain in the backside.
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