Using retroarch to run MAME is never going to be optimal because their adapter layer is heavier weight than MAME's Windows and SDL interfaces and not designed for MAME anyway. You just have to live with that.
And because it's a quite-extensively modified fork of MAME, asking the retroarch guys what's wrong is going to be more fruitful than asking MAMEdev.
I'll just conclude once again: if genuine MAME plays the games better, play them in genuine MAME.