The fix is to do a full binary install. Due to large changes in retropie-setup the way stuff is launched has changed and installing an individual emulator from source will not suffice I’m afraid. BTW there is no need to install mame4all from source – the binary is up to date and there is little development to this code.
Although hacking the es_systems.cfg may fix it, you will likely run into further problems – the _SYS_ is used by the new runcommand launcher.
BTW I assume you manually typed the error above – there is no recommended.sh – it is called runcommand