For others with the same problem – I found a workaround – but not ideal – solution. No idea if this was introduced in 2.6 or not.
For some reason, those retroarch.cfg files in individual system’s folders don’t seem to be pulling in any additional input lines. All of the other lines seemed to be working fine.
I was able to get the secondary configs working by calling them with the –appendconfig command line switch.
You have to change the command line in order to do this. For GB it was in the es_systems.cfg file; and for NES it was in the emulators.cfg file I believe. I also had to remove the #include line at the beginning of these individual config files.
For example:
OLD:
/opt/retropie/supplementary/runcommand/runcommand.sh 0 “/opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/neslibretro/fceumm_libretro.so –config /opt/retropie/configs/nes/retroarch.cfg %ROM%”
NEW:
/opt/retropie/supplementary/runcommand/runcommand.sh 0 “/opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/neslibretro/fceumm_libretro.so –config /opt/retropie/configs/all/retroarch.cfg –appendconfig /opt/retropie/configs/nes/retroarch.cfg %ROM%”