Is this an integrated VP support thing? If so, disable it. Run PinballX as Windowed, Full Screen then configure VPX to run exclusive full screen. Problem solved.
Integrated support copies over certain PinballX settings for use in VPX. It makes it easier to get beginners up-and-running, but after a while I think it gets in the way and creates problems as it is literally overwriting screenres.txt and registry keys. At some point to enable your customizations or other advanced features you must take the training wheels off and learn how the software functions. Often getting certain Stern S.A.M. system games running or enabling full colorizations on DMD requires directly editing the Windows registry. PinballX and VPX are two different programs. You do want to run VPX as exclusive, full screen. You don't need to run PinballX as exclusive, full screen, It is recommended that you don't. But even well prior to v2.91 I found that PinballX just operates more smoothly windowed.