The problem was that when I unlocked the vehicle from either the remote FOB or the door key, the driver door would always unlock and then immediately re-lock (the door lock dance). You had to be quick and open the door as soon as it was in the unlock position. Alternatively, you could hit the unlock twice which unlocks all the doors, then open the driver side rear door and reach in to manually unlock the driver door via the manual rod/button (not the master switch). The door lock dance was the most consistent symptom, but occasionally it would throw in a random one like spuriously locking or unlocking the driver door when I least expected it. I was sure that one day it was going to lock me out with the key in the ignition. In fact, the guy I purchased the car from warned me of that.
The cause was that the driver door lock manual rod was excessively bent such that it didn’t align well as it passed through the hole (ferrule) in the door panel. This was causing excess friction and not allowing the manual rod to travel its full length needed to make up the electrical switches inside the door lock actuator. I surmised that this was from careless removal and handling of the door panel which allowed the manual lock rod to be bent out of factory position. There were obvious signs that the door panel had been removed in the past.
The solution was simply to bend the rod back into its factory position so that it passed freely through the ferrule with the door panel installed. Even with the door panel off, the manual rod did not show obvious signs of being excessively bent and it has several factory bends in it already. But there were telltale signs once I actually knew what the problem was. Because it was dragging as it passed through the door panel ferrule, the plastic on the stem of the door lock button had lost some of its shine and its up/down travel distance was less when electrically actuated than if it was manually operated by pushing down or pulling up on the door lock button. It also didn’t travel as far as the other door lock buttons when electrically locking or unlocking it.
To troubleshoot this or similar door lock issues, I would suggest doing some simple checks before going on to more complex electrical or computer related troubleshooting. Remove the door panel from the offending door, then remove the door panel switches from that door panel and reconnect them to the wiring harness so you have full functionality of the switches without the door panel on. This allows you to visually inspect the door lock actuators and linkage as you operate them. Operate the locks manually and electrically (from the FOB, the door lock switch and the manual key driver door only). There are 2 linkage rods in the driver door to give you trouble, one for the door key lock and one for the manual button. Check for broken plastic retainers on the rods, ensure full unimpeded travel of rods (one of them has a metal clip which allows for travel length adjustment too.) On my car, the door locks worked correctly with no more door lock dance once I had the door panel removed and the switches hooked back up. So it was pretty obvious that it was related to the door panel.
I guess the moral of this story is be careful and don’t bend the manual lock rods when removing and installing door panels. And certainly make sure they operate freely after door panel install, there should be little to no resistance when pushing/pulling the manual door lock buttons.