Okay never mind, I got it to work, in windowed mode. I toggled to run the program as administrator, because I ddidn't think it was using the config file at all. Then it finally ran in windowed mode when I selected fullscreen=0
And in windowed mode, there's no flicker.
Sorry for the trouble, but at least it's here in case someone else has a problem
If I figure out how to run it full screen with no flicker, I'll post an amendment.