The one and only solution.....You MUST reformat.Period.
I had the same thing happen....windows flagged me down that malware or trojan infected my registry.I had these anti-viruses scan and try to detect for two days...nothing.
1.PC Tools Anti-Virus
2.Threatfire
3.Spybot
4.Adaware
5.Bitdefender
Nothing worked because the virus had embedded itself so deep within the registry.....it could not be found,let alone removed.So you must reinstall windows.