Having same issue v2.6. before I ran the “sudo ./retropie_setup.sh” the roms were working. Not sure why after running “1 Binaries-based INSTALLATION” cause this issue. These rom I had where from 1999. I tried with Mame4All Rom’s and same issue.
Upgrading from 2.6 to 3.0 can be awkward in terms of config files – can you just use the RetroPie 3 image instead?
Ultimately that’s what I did; I just reformated my SD card with the 3.0 Beta 1 image (which was current at the time) and went from there. No further problems, aside from having to copy over all my roms for all my emulators and re-set controller configurations for each of them.