The only tests affected by antiviral drugs are those that detect the virus itself, e.g. culture of a lesion--and that's a sign the drug is working, i.e. suppressing the virus in the lesion. The anti-herpetic drugs do not affect blood test results at all.
So I also am somewhat confused by your test results. Conceivably your wife's genital area culture was mis-diagnosed as HSV-2 and really is HSV-1. The only other explanation is that your wife acquired HSV-2 while on famciclovir (Famvir), which is exceedingly unlikely; and she would have had to have acquired it from you (unlikely with your negative HSV-2 blood test) or from another partner--and presumably you would have said something if that was likely. So I am left with the possibility that one or the other of you has had false-negative HSV-2 results on your HerpeSelect tests. That isn't common, but it happens.
Bottom lines: 1) Ask your wife's HCP and/or the lab to double check the HSV-2 determination for her positive culture. 2) If her isolate is confirmed as HSV-2, you both should have repeat testing. If your provider(s) send specimens directly to Focus Technologies (manufacturer of HerpeSelect) and explain the situation, they may to special testing, such as Western blot, at no cost. Alternatively, request a Western blot test by a reference lab, such as the University of Washington labs in Seattle.
PS: Just curious whether you are sure your wife is on famciclovir and not valacyclovir (Valtrex). The dose you describe is a peculiar one for fam but the typical one for val. Also, famciclovir must be taken at least 3 times a day to be effective; even a large dose like 1000 mg likely isn't going to be effective if taken only once daily.
Good luck-- HHH, MD
I think I mistated, or was confused; she had previously only used Valtrex for the oral HSV-1 but then started taking Famvir during the vaginal outbreaks, so I was not 100% sure as to whether she was on Famvir or Valtrex at the time of the culture diagnosis. When she received the HSV-2 positive culture it was during her second outbreak (second one within 2 weeks). She then had a third outbreak two weeks later and has had nothing since (been about 8 weeks since the third outbreak). The first outbreak was the worst and each one has been less painful and less in duration.