Hi Tony,
What you are measuring with this particular setup is giving you sort of false reading. By using the primary as a sensing coil, you will only see the primary in a freewheeling effect. It is well known in the art that pulsing a transformer will always output an AC signal no matter which side is pulsed. So, in affect, your sensing coil is botching your experiment and true measurements. It is possible to measure without the sensing coil and just using chokes by using a suitable shunt resistor on the negative plate. You may have to calculate, though, to get the real numbers. A resistor will work with both the oscilloscope and any voltage meter, but you may want to research on the web the best way you can find to accomplish the task. I myself do not have an O scope but this is what I use for measuring high voltages from 10-30Kv...
(http://www.electronicrepairguide.com/high%20voltage%20meter.jpg)
I got one off eBay for 20 USD...