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I guess the problem could be with the microswitch which senses the key being turned to the lock position. I believe the convertible top will go up and the car will lock if the key is held in this position. It is odd that it happens randomly, and that the central locking button on the dash also won't work sometimes. I would have thought that a problem with the alarm control unit would more likely cause faults like that. Any dampness under the left hand seat (driver's side in the US)? That's where the alarm unit is located.
It sounds like a microswitch within one of the door locks which senses if the door is open or closed is broken. The system 'thinks' the door is open, so after locking it immediately unlocks. As a temporary measure, you can use the emergency locking procedure. Turn the key in the door lock to the lock position and back 3 times in quick succession. It may also work if you press the remote button 3 times.
Try looking in the input signals of the alarm control module on PIWIS. These are from PIWIS2 in Simulation Mode. Select Alarm from the Overview screen, then Maintenance repairs, and choose Input Signals.
It is anyone's guess, I'm afraid. They used to release updates every two years or so, but these systems are up to 14 years old, so I guess they will stop supporting it at some point. The updates are seldom up to date anyway. If you put your DVD in a PC and check out the database file dates, they will likely be older than 2013.
The latest USA map for PCM2.1 is indeed 997.044.904.51, which is mid-2015. Because you are running the 2013 map, your system must have been updated in the past, so the new map disk would be plug & play. PCM version 5024AD1 is software level B. You may also have read that there is a Level C update, which yours must have had. However, when you update from Level B to Level C, it only updates the Navigation Drive, not the PCM head unit. If you view the software version for Navigation, it should show Actual:00179436, which is Level C for the Navigation drive.
It is possible that the Sport Chrono module has slipped into transit mode. It happens after a flat or disconnected battery, and can happen to various modules. If that's what has happened, it needs waking up by running the handover routine with a PIWIS tester.
The Headlight Beam Alignment module is located in the right hand side of the dashboard, under the passenger airbag. (LHD car). I don't know if it would cause your problem, but a common failing on Litronics is the plastic level sensor arms on the suspension. They break, or become detached.
I doubt the problem is the alarm/immobilizer. The immobilizer inhibits the fuel pump, ignition, and starter motor. Because it is cranking, the immobilizer is inactive. I suspect the root of your problem is the battery. Low voltage causes all sorts of problems.
On early 986/996s with DME5.2.2 (non-eGas), pin 60 on the DME (Software Voltage) is used when re-flashing the fuel map with a PST2. At the start of the flashing routine, the PST2 applies 12vDC to that pin, and it disconnects it when the flash is complete.
If the car started, then it has recognised the immobiliser code, so it sounds to me like the programming is correct. Do you have the alarm siren? Is it the siren which is going off when you remove the key? The siren is to the right hand side of the battery, as you look at the car from the front. If you have the siren then I suspect it has a bad backup battery inside. With the ignition switched on, unplug the siren. Then see if the alarm goes off when you switch the ignition off and remove the key. You might get a beep from the alarm horn (a separate horn on the other side of the battery) when you lock the car, because the siren is disconnected.
You need to enter an activation code into the PCM using a PIWIS tester before loading the new maps.
I think you need option 666 or 619 for Bluetooth phone. 619 can be retrofitted, which is less expensive than 666. By the way, you can't update the system to v2.24 in one step. You have to update to v2.23 first. Your dealer should know this. I would try to find one who knows what they are doing. The 619 Mobile phone preparation retrofit involves fitting an additional microphone and entering an activation code for the Bluetooth using a PIWIS tester.