Thanks Tom, but I'm not confusing them. There is nothing for 90% of my tables in Pinball X for the DMD, I have a few low quality videos for some of them though. In Pinball X, Game Manager, everything is set to hide except Toppers on some tables (since I have videos for those). Show Backglass = Hide, Show DMD = Hide etc. It 100% is someone loading the ACTUAL standard non Freezy DMD when launching from Pinball X, even though the Rom has it unchecked. The Freezy external DMD is loading as well, it's just "under" the standard DMD. It's definitely very very weird.
This only started happening once I changed all my tables to use the external Freezy DLL and colorized dmds. I'd say it was a bug there, but things play fine when launching straight from VPX or Even Popper, so it's definitely a Pinball X thing.