I have no idea. Herpes is not a disease that is carried in the blood stream in adults with herpes. It might be used to diagnose a newborn who might have herpes in the bloodstream.
I think the most likely explanation is that both your doctor and ID doc got mixed up about the use of PCR. PCR should be used to detect virus in a LESION not in the bloodstream. A blood PCR has absolutely nothing to do with viral shedding. They are mixed up here.
I hope that your western blot provides clarification for your herpes status and that you will let me know when you get your results.