Russ,
Here's what I was talking about on Skype, but couldn't recall the terminology at the time.
This phenomena has me very confused as to what really happens in the VIC cores since we are using DC biased unipolar pulses. The only thing that makes sense is what you mentioned about the relaxation time allowing the core to neutralize. So if I were to take a WAG at this thing, I would say you find the frequency, then adjust the DC bias and/or the gate time to allow the core to partially zero itself. Otherwise with no gating, the core likely walks into saturation on each half cycle. Maybe this is by design and maybe it's something we have to compensate for, I don't know at this point.
With so many turns of rather small wire (relatively large resistance) on the primary, maybe the magnetizing current is substantially reduced and this doesn't become a problem. Then again, if we have exact voltage and have calculated exact resistance, we are actually trying to walk the magnetizing current up to that fixed I = V / R level. If we do that, then I speculate we are indeed passing through a DC bias to L2 and to some degree L1 and the secondary, though at reduced levels due to the core gap.
Here's some more information on the subject--take a deep breath and jump in:
http://www.consult-cpr.com/Additional%20Pages/Eng%20LinksB7.html