Nothing changed as far as the paths. All of my Mame files, roms and artwork is all on another hard drive- so that I wouldn't lose them if something happened to the root drive. The only thing I did was back up my MameWah files and layouts, then when I reinstalled it- I dropped them back into the folders.
But it didn't like that.

I had refreshed the games list several times, and the "Generate Custom List using Filters" never worked, but this morning it does. Weeeeeird.
Minwah- the .lst files work, but the list names didn't carry over and I don't remember which list was what. Isn't that all in the old emu1.cfg file?