This might be a bad latch. I am having a problem with mine. First, my locks did all lock, but they were opening and closing at random times. I also then noticed that the passenger door, when opened, did not turn on the courtesy light. I posted on here, and a lot of people told me a bad latch. I took it off yesterday, and did a bench test on it and found it was bad. This could be your problem.
I ordered a new one and did an on-vehicle test by unplugging the old and plugging in the new - same issue. When sitting on the seat the new latch only SuperLocked, not CDL locked. I've got an Electrical Troubleshooting manual on the way for my year - the RAVE manual that I grabbed was for a vehicle year too new, or I'm not using the indicies correctly..
Solution: the PO had a new unit installed - believe it or not, they had not hooked up the "Single Wire" connector to the new door locking mechanism. Once I did this, the upper tailgate lock worked again and the "sill locking" and CDL locked as well as the SuperLocking function.
Testing for the "Not Hooked Up Single Wire" - open the passenger (or probably any) door: Does the footwell light come on? Puddle lamp? If not, it's either that this "single wire" has broken or was not hooked up. If the light comes on but the CDL function does not work, then you're probably looking at a bad opener servo motor.
With the door links not working, Did you notice it not closing by a mm or two. Also did you have a lot of wind noise on the highway near the top of the door frame. What did the door links cost if you done mind?
Hey Skuyler - no sir, Locks worked okay otherwise and I was able to close/open it just fine. No wind noise. If you've got a problem like that, create a new thread here and let's make sure that you get some pictures up and I'll bet that folks here can help!
Each NEW Passenger or Driver door actuator is about $250 - it's expensive to do new ones, but used ones are too difficult to test unless, in some cases, you cut/splice wires before installation. If it shows up and a motor is burned out or a relay is trashed, you're just SOL unless your vendor will take it back.