Not many have reported such an issue iirc. If its been that way since the moment you flashed to HF6 then perhaps the flashing went wrong, otherwise sometimes the nubs can get stuck in joystick mode after exiting Mupen64 for example.
In HF4 upwards you can reset the nubs from settings>nubs>restore default settings for both nubs
This was replaced by Caines nicer UI for nub settings in a later HF (developed here ) and that maybe what's in HF6.
In which case go to:
settings>pandora nub configurator and hit the 'reset nubs' button.
Hopefully that will help. If not its probably best to reflash again.