Assuming you're film seps all register to one another (sometimes a printer can output a film out of registration due to roller slippage), or add enough trap to the overprint colors or enough choke to the underbase to compensate, about the only thing you can do is as mentioned earlier, hold the screen down firmly to the platen as you tighten the screen clamps. If it's still out, loosen the clamps just enough so that you can tap the screens with a hammer to nudge them into registration.
One other thing to check is warped screens. If you have enough warp in a screen it's possible you'll never get it to register to prints made from screens that aren't warped.