In MLB power pros the analog on the baseball bat doesn't stay still but has little but existent up and down movement.Nope, only for those I mentioned.
VBAGX and SNES9XGX seem to be working fine for now (at least the character doesn't seem to go down like in those ones).
Just to be sure, try to play an FPS game (like Doom on both emus) and let me know if the character is being held back.
Then if that is it, it's the controller and not Homebrew apps.