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#11
Are you running MucAfee, because that could cause the problem itself? I would uninstall the worst bloatware AV out there and install Microsoft Security Essentials.
Like the worst infections MucAfee requires a special removal tool to get it all out: Uninstallers (removal tools) for common antivirus software - ESET Knowledgebase
This was specified in the Troubleshooting Steps for Windows 7 so you must have missed it. Did you do the RAM and HD tests yet?