Ok, I'm going to leave the solution here for anyone who may need it in the future:
if using the US rom (NES), set User 2 to NONE instead of auto. if using the Japan rom (Famicom), disable User 5 instead.
Further explanation:on NES, player 2 port acts as expansion port, including arkanoid paddle in this case (using mouse) on Famicom (when loading Japanese ROMS), expansion port is on a dedicated port which is mapped to User 5 on fceumm.
this should resolve this issue and any other confusion with nes/famicom expansions