My receiver has a fair amount of slop, so I would never notice something like this. It would just center itself. Is it possible that your 2" opening is not totally square to the back of the truck? And by locking the receiver into the hitch you are forcing it to be at a bit of an angle? Or there could be a degree of error in the actual receiver shank/hitch attachment.
I've not heard of anyone having the L brackets at different heights side to side, might be interesting to shoot Equal-i-zer an email and ask, I'd be interested in their response.