If you have -listxml vs ROM Folder selected as your list-generation method and you're pointing to the correct version of MAME (when the -listxml option existed, post version .84 I think) AND your ROM folder is correct in MAMEWAH Config, then everything should work fine. However, you want to make sure you delete any emulator lists first, as they don't get updated in MAMEWAH Config when you re-generate the default list (In MAMEWAH they do, which I always found annoying).
-Steve