Sounds like an issue with one of the wires or a connection. As you set the control assembly back into position the wires in the harness bend and stress, perhaps enough to compromise the integrity of either a ground wire/connection or the power wire/connection. Also, there could be a damaged ground or power wire coming in.
You may want to pull the power window control again and carefully inspect the wires and connections, checking to see if anything is loose, etc., and otherwise use a multi-meter to check for continuity through the switch (es) as you jiggle that switch’s wiring. You could also check the wiring coming into the door for voltage, again, while jiggling things around a bit, to see if you have a damaged wire in the sheath routing from the door jamb to the door.