Yes I do have Mame 135 command line which is what Mamewah is using. I also have Mame 32 but its completely separate from mamewah.
The roms are pointed to the right directory and most of them are working through Mamewah, but a handful of them aren't even though they work fine in Mame32.
EDIT: So I tried running Marvel vs Capcom with Mame 32 and then just the Mame command line. Mame 32 will run it but Mame command line won't, it says:
mvse.03a NOT FOUND
mvse.04a NOT FOUND
ERROR: required files are missing, the game cannot be run.
So I guess this isn't a mamewah issue at all. Does anyone know the difference between Mame .135 and Mameui132?
EDIT AGAIN: After some monkeying around it turns out to just be missing clones, still seems kind of odd though.