are your extensions capitalized? .NES will not work , but .nes will
Capitalized extensions are set to be acceptable in /etc/emulationstation/es_systems.cfg and should work fine. Below is an excerpt from the NES system entry.
<system> <name>nes</name> <fullname>Nintendo Entertainment System</fullname> <path>/home/pi/RetroPie/roms/nes</path> <extension>.7z .nes .zip .7Z .NES .ZIP</extension> <command>/opt/retropie/supplementary/runcommand/runcommand.sh 0 _SYS_ nes %ROM%</command> <platform>nes</platform> <theme>nes</theme> </system>