I have exchanged a few emails with Scott at boldtower and confirmed that I have the correct frame.bin files. Re-download them from his site if you want to be sure that you have the correct ones.
Scott sent me a copy of his .exe for a quick test.
With his .exe and the correct frame.bin, I can run MACH# and it plays well, but then I get the "...Stay Put" error at the high score screen after a game. I'm not sure yet why my .exe does not want to work with it. I think I will try starting over from scratch with regular mame 0.79s and adding the patch again.
I reformatted my mpegs to match the resolutions that Daphne CVS is looking for, and tried to run them that way. MACH3 starts up OK and displys the High Score screen. I can add credits, but I can't seem to get the game to actually start. None of the defined keys seem to start the game. Hitting '2' causes the coin drop sound to play, but an additional credit does not appear.
FireFox starts up, displays the first frame of the mpeg and that's as far as it gets. When you start it, Daphne says that the inputs and VLDP are not working yet.