Also from what I remember, lasers, even fixed ones, have a small amount of "gimballing" could it be the lasers are correcting the beams but the railgun isn't?
even with fixed pulse lasers you have this problem.
the way i tested it on my Anaconda:
get some containers of cheap goods (fuel, algae...whatever)
SC a bit out to have a place for your own.
jettison the canisters, move away about 700m
now get your weapons out and try to get all reticules to snap on target.
the weapon aid works a bit better on ships (which are of course bigger), but you get an idea how far it will "track".
i don't think you'll get more than two weapons to lock on the canister.