I notice that you have your Map or SW List File for n64 pointed at GameEx\MAP FILES\[Console] Nintendo 64 - USA.map. In that mapfile, all the roms are listed as zipped. GameEx is pulling the file name of the game from it.
If it's failing because of a checksum, it means it is comparing to some known rom(s) checksum. The "Retrode" is possibly adding some minor data (or alternatively, the Retrode isn't, but the known-good roms had some bookkeeping metadata type stuff added during their dump). My guess at least!