Ahh, ok...
I think you've stumbled across a recent feature (auto show dmd media if no dmd found, from PinballX 5.03), maybe it's not working quite right for you if the games launched do actually use a DMD. Anyway, try turning off that setting;
In Settings.exe go to Display Settings and set 'Auto Show DMD Media' to No.
Hopefully that'll do the trick!
(oh, and a link to Database Manager is in my signature if you want to give that a go anyway)