Replying to this old topic with the solution that worked for me, after finding this question via google with no reply.
It's likely your left/right triggers were configured incorrectly. If they're configured for minus axis, retroarch believes they are held down when the game launches and everything acts weird. It's likely the retroarch menus are un-navigable as well.
To fix the problem, go to "configure input" again and make sure left trigger is "Axis 5+" and right trigger is "Axis 4+". If they're negative the emulator thinks they're held down and that's causing the problems.
Hope this helps anyone else coming across this problem via google.