Have you used the Digi-Code Universal Safety Beam Sensor Replacement Kit CR-2149 (123 REMOTES sells those) by any chance ? It is a universal beam sensor but the install procedure for Stanley has an additional step: <q>Clip the BLACK jumper wire sticking out of the back of the new receiver unit.</q>
Did you do that?
Also, do you see both red LEDs, in the sender as well as the receiver? The red LED on the sender is on all the time when power is ON, only the receiver's LED is an actual alignment indicator. The door behaves as it would when the sensors are not aligned, that why I ask.