If you have only use parent roms selected in maximus arcade, and don't have a complete set, that could be the problem, same with ignoring clones, same with ignoring bad roms.
If you uncheck those checkboxes and see them on your list after all, it's probably because you are using the alternate rom to the parent rom (I think I am wording this right).
For instance, if I am running Street Fighter 2 (rainbow version) it will run fine in MAME, but if you scan to use only parent roms/disable clones, it will not show up on your list as it is not the "main rom", because it isn't.
Are you working with a complete MAME set of roms for the version of MAME you are using?
Hopefully some of this makes sense, I am not right next to my arcade with maximus on, to tell you the right settings, but that may be your problem. Just a guess.
Not too long ago, I was wondering why Pac man wasn't showing up, turns out I guess its parent rom is Puck Man. Puck man was there!