PinballX screen settings look odd. Relevant parts;
[Topper]
monitor=2
[Display]
Monitor=3
[BackGlass]
monitor=2
From your picture it looks like the playfield ([Display]) should be monitor 2, Topper should be 3 and backglass don't know, maybe 1 (but definitely not the same number as Topper. Try changing those number im Settings.exe, Display section.
You do have AutoPositionB2S=True set so i'm hoping once the screen config is sorted out in PinballX that will then copy over to VPX. I've no idea about the DMD driver error (i'm a virtual DMD user), but take things one thing at a time.
So, i'd suggest updating PinballX and post a screenshot of your windows display settings as suggested by Mike, then try changing the display numbers around.
(database manager won't have done anything with your screens, but maybe there was a windows update or something that messed the numbering up)