What I got from your description was that you took some corrective actions, fixed some reg entries, but found things unfixed later. I don't know what actions you took but it sounds as if you're being toyed with by an active agent (virus, etc.) or system restore, or both. (Sounds a bit like an evil helper object.)
If system restore is active and it senses an inconsistent state from deletions or whatever, it'll restore files from the last checkpoint. If that checkpoint contains the problem then it'll keep coming back. To get around this turn off system restore, do your things, if the problems come back then something else is involved.
No, system restore won't save the new fixed files in safe mode, but if it decides things are inconsistent it will write over the fixes the next time you boot in normal mode.
What scans have you tried? Hijackthis?
Did you find a barbecue?
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There are a vast number of people who are uninformed and heavily propagandized, but fundamentally decent. The propaganda that inundates them is effective when unchallenged, but much of it goes only skin deep. If they can be brought to raise questions and apply their decent instincts and basic intelligence, many people quickly escape the confines of the doctrinal system and are willing to do something to help others who are really suffering and oppressed." -Manufacturing Consent: Noam Chomsky and the Media, p. 195
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