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In my experience (admittedly limited - only 3 systems), those annoying security popups ("Unable to open filename, file is corrupt, click here for virus scan" or similar message) can often be cleared manually. In all three cases, I was able to boot into safe mode, identify the unwanted startup entry in the registry, and remove both that entry and the associated directory. All three systems were normal after a reboot.

Have some patience. Each of those three systems took at least 5-10 minutes to present a safe mode login, almost as if the malware was attempting to block it.