Quick update. I found that if I launch the table through PBX, then wait for the "Loading" screen to disappear, Alt-Tab to bring the playfield into focus, then hit "q,q" to quit the table (but not exit back to VPX, my exit emulator key is "e"), then launch the table (play button) again from within VPX, then everything works (playfield in focus and DMD on top of backglass). So there may be a way around this.
This is also the same behavior if I launch the table manually from within VPX and not PBX.
Also just realized I forgot to attache my settings, so here you go.
Thanks