I had this same issue with Don's Hyperspin Tools despite a pretty new system. If you're trying to create many separate xml lists, then I would vote +1 for ROMLister.
However, I realized later than I'd like to admit that I was missing one small setting that completely fixed my problem (I was trying to just have the wheel display games I have roms for): In HyperHQ, click on wheel settings and bring up the MAME emulator (or whatever you're trying to build). Go to the Navigation/Themes tab, and on the very right side, ensure that under Wheel Filters you have "roms only" checked. That changed my wheel from listing every game in the overall xml file to just the ones I have roms for. If this is overly simplistic and you've already done this, please disregard.