The central locking is intermittent sometimes works when setting alarm other times does not? when alarm is disarmed and unlock the car with the key it sometimes unlocks all doors but usually only the drivers door? when sitting in the car and try the lock button it takes a few attempts before it will activate the central locking?

Check fuses, remote control battery, try to push "unlock" button 5 or more times. If it won´t help, you need Tech-2 diagnostics.

Door Key Switch
The BCM monitors the door key switches in order to disarm the CTD system. When the lock cylinder turns in order to unlock the door, the switch grounds the disarm input to the BCM.
The key lock input to the BCM is probably missing , BCM doesn't see it . So it think's your breaking into the vehicle. Did you try the passenger door to see if it will disable the alarm .
The BCM - body control module ! Electronic -computer !
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Content Theft Deterrent (CTD) Does Not Disarm with Key Lock

The factory service repair manual has a 23 step diagnostic procedure . An you would need a factory scan tool to find the correct fix.
Turn ON the ignition with the engine OFF.
With a scan tool, observe the door key switch parameter in the Body Control Module (BCM) security data list.
Does the scan tool display INACTIVE?

Locking the Vehicle Without Arming the System
Use one of the following procedures in order to lock the vehicle without arming the system:
• Procedure A -- Lock the vehicle using the manual door lock knobs. Close all the doors.
• Procedure B -- Close all the doors. Use the key or the power door lock switch in order to lock the door. The doors must be closed prior to locking the doors for this procedure.
Disarming the System
In the arm initiated mode, the following conditions are true:
• The security telltale is ON.
• The doors are open.
In order to disarm a system in the arm initiated mode, perform one of the following procedures:
• Press the power door lock switch to the UNLOCK position.
• Press the door unlock button on the key fob.
In order to disarm a system in the arm delay or the armed mode, perform one of the following procedures:
• Use the key in order to unlock one of the doors.
• Press the door unlock button on the key fob.
Deactivating the Alarm
In the alarm mode, the following conditions are true:
• The horns sound intermittently.
• The headlights and the park lamps are flashing.
In order to deactivate a system in the alarm mode, perform one of the following procedures:
• Use the key in order to unlock one of the doors.
• Press the door unlock button on the key fob.
• If the vehicle control module (VCM)/powertrain control module (PCM) receives a valid Passlock™ ignition key rotation.

It sounds like the key sensor in the drivers door is malfunctioning, the drivers door is the only door that can enable/disable the alarm, if you try to unlock any of the others it will trigger the alarm.

Sometimes with my Kia I have to (without opening the door), cycle lock and unlock several times before the alarm is disarmed.

Have you tried this is succession, with all the doors locked:-

put the key in the drivers door, turn to lock and then to unlock, the alarm should disarm.

Also, if any of the door locks are jammed, the alarm will still activate when you try to unlock the drivers door.

If that fails and the alarm still activates, then it's a problem with the key sensor in the door.

The alarm will time out and turn itself off after a minute or two when it is tripped. This turns off the alarm, not just the alarm horn.

Are you saying that you can't unlock a door from the inside by hand?

Here is what I do on my 95 Cirrus I also do not have a keyless remote (well I do but is broke) and after frustation after frustation trying to disarm the factory alarm I find out that by unlocking the passenger front door with the ignition key from the outside will disarm it you may have to try few times before it's disarmed you need to make sure that the blinking red light stops blinking and all of the locks on all 4 door are up or unlocked, this is what I been doing for 3 years now and that's how I disarm the alarm on my car, I hope this helps.

try locking and unlocking the car with the key 3 times slowly ,other than that i have no idea ?? another trick is to disconnect battery and join the cables together for a few minutes to discharge any capacitors that may be holding a charge in the computer..Only other thing i can think of is the main dealers who have the right connectors and software to re set it all .sorry i havent been of any help

the body control module may need a software update..check with your local dealer

Time for a new key fob.

with any BMW they have their problems, one is the central locking/immobilizer, the central locking is linked into the immobilizer and vice versa, the immobilizer takes it signal to disarm from the central locking and the ignition key ring. (chip in the key) if one of these starts to play up it has loads of consequences this being one of them. they all need to work together for the system to work properly. you would need to read the alarm and immobiliser codes using an ob2 tool that can detect them, and find the fault some problems it can be the drivers door sensor in the lock this is the main door as its drivers side and it controls all other doors on the central locking. if the switch is worn in any of it movements the system will not know the door has been opened, this does not work on the interior light as that is a switch in the door frame. the door lock is lock unlock and deadlock with key with remote fob its also arm disarm alarm and immobiliser. i have seen in some models there is a sensor auto lock so when you walk away with the key the doors lock automatically all lease parts work together. any one having a problem can cause no signal to be sent to the others in the system to start engine .

I'll assume you used the remote here (like most of us do) to arm the alarm. Try turning the key in the door lock - turn it to lock the car (which arms the alarm), and then unlock it (which should disarm it). Do this a couple of times if need be, and it should disarm and allow you to start the car.