Still having this problem myself. It's almost definitely not a hardware issue and it certainly is <not> happening to the right nub, only the left. I tried changing the analog input of Mupen to the right nub and it worked as it should. I'm working on testing Android to see if the error persists inside it.
This is the only problem I've been having with my Pandora but its become excessively annyoing; N64 games are completely unplayable.
I'm playing N64 games width the dpad now and it works well for me. I also played around width the calibration values in the mupen config file:
CALIB LEFT[0]=1.0
CALIB LEFT[1]=1.0
CALIB LEFT[2]=0.0
CALIB LEFT[3]=0.0
Using this values the left nub works well for me, but i prefer playing n64 games width the dpad