What I did is setup 2 additionnals emulators, with retroarch too, default command line with the core I want, and just one associated platform.
So i have Retroarch named retroarch, for all of my platforms that works that way, retroarch named Atari 7800 for only the atari, and retroarch Mega drive for only the mega drive, and it works like a charm, and It's completely transparent.
Short story : If you have several associated platforms with several cores and one is not working, just dissociate it by creating an other emulator only for that platform.
Thanks for the quick help guys !