I'll explain the entire situation if you like. It has to do with some unexpected behavior in the fpga-to-output-driver level shifter circuit I posted about a while back, the one with the C-W multiplier tapping off the switcher. It took us a while, almost half an hour, to figure out what was actually happening. Since you understand electronics so much better than I do, you will no doubt figure it out instantly.
I trust that other posters will refrain from making suggestions for a short time so you can have the problem all to yourself.
Wanna have a go? I'll post the problem, and you explain what's happening and several possible ways to fix it. It should be easy for you, as I've given half the answer away already.
OK?
John