In my case the problem was a trojan file called klgempth.xiv
It took Microsoft nearly three weeks to find it. Most of the diagnoses
was done driving me with wnddbg and supplying huge .dmp files. It was
extremely interesting. Once the Microsoft scanner was updated other
people found variants of the same malware. It's a mystery where the
infection came from. If I submit the file to Virus Total about half of
the scanners now find the problem. Some of the "big league" scanners
like McAfee and Norton still miss it.

You may have removed the malware with your rebuild.