I think you must have configured Mamewah incorrectly.
If you have .89 roms, running MAME32 Version .89, then you should get the commandline mame version .89 and the roms will work.
Additionally, you will need to configure Mamewah to pass the rom names correctly to command-line mame. If NONE of the roms work, then chances are, you have incorrectly configured Mamewah... if only some of them have a problem, then it's probably MAME itself.