Well son of a b**ch
I thought the RetroArch Launcher was more stable. Well, it's not, the second I changed from Snes9x mainline to Genesis Plus, it all goes to hell.
I was really hoping for more stability, maybe Haxchi + CFW really is the cause, I'd install CBHC if it wasn't so risky.
I'm pretty sure rolling back to 1.4.1 or even 1.5.0 would prove more effective since this bug is persistent and easily reproduced. Even using the RA Launcher didn't help with core swapping. But tit seems, the Ogg Vorbis aspect is causing it.
I'll stick to the PC port until this is resolved.