When I tried to drag and drop ZIPS or even unzipped ROMS into the scanner window on 3.62b it wouldn't rebuild the roms like it usually does.

I manually merged the roms and it detected that the now manually-merged roms were no longer missing.

Ironically, when it tried to rebuild missing sets from the scanner window it caused the zips in the ROMS directory to have an invalid zip header (and the ZIP file size was only a few k instead of the correct size).