jroberts, I deleted all *.prf files in the output\preferences folder except Calibration, Joystick Settings, and Keys. After rebooting I ran X-plane 11.25, "new flight", and the pop-out windowing problem was solved. I changed some Graphics settings such as visual effects, and windowing still worked fine. I exited X-Plane a couple of times, went back in and flew briefly, and the pop-out windows behaved correctly each time.
I'm considering this fixed. I still have the *.prf files from when the windowing problem existed (saved outside of X-plane) if you would ever like to see them.
Thanks for pointing me in the right direction.