Leiradel has been working on fixing the issues with retroachievements on RetroArch. I can confirm that the fixes so far have stopped achievements unlocking when starting a game and also now GBA achievement’s work. I’m using the MGBA emulator.
To get these working just update RetroArch from source in the retropie_setup script under main cores.
There is also a github repo here to upload any savestates you have just before an achievements should be awarded and it doesn’t for what ever reason. This will help Leiradel when trying to fix any achievements issues.