Toad alarm on vw transporter

Fob didn't work so the alarm immobiliser was armed and active when the locksmith opened the car - with predictable results.

Fob still not working - broken or needs new battery. Have you fitted a new battery into the fob?

The alarm immobiliser will probably remain armed until the doors have been locked and then unlocked with the fob.

There is a small chance the system can be fooled into thinking it has been disarmed by disconnecting the battery (overnight if poss) and then with the door open and the ignition key in and turned on, when the battery is reconnected it might be possible to start the engine...

Temporary fix is to not arm it.
1. Unlock car with key fob or drivers door tumbler.
2. Open drivers door ( to avoid it automatically re-arming)

3. Lock the doors manually. Not with power door lock switch , key fob or key.

4. Close door.

Would help if I knew what year make and model of car you have and if it’s a factory alarm or aftermarket and brand.

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.

I would look into getting a new key fob and having it programmed to the vehicle. If not tben use the key and lock unlock the door to deactivate the security

This could be your micro switch in the door lock itself , by a vw golf type four and other modelss you have an automatic locking function if you unlock your door but don't open it and most of the time it's the passengers door as it is used the least.firstly check the wiring to the lock and between the door and the body then checck the micro switch on the lock if its correctly seated and if its make a click when you press on the metal arm .

The alarm is armed if keyfob is used. So you must use the fob to disarm alarm first. So someone can not unlock and open door without keyfob or alarm will be set off.

For starters you can unflatten the battery!

I don't see where you have any choice but to unlock the doors with your key. If your fobs have good batteries, then the problem is with the alarm system, which can't be accessed until you unlock the doors. I'm not sure what the procedure is on your particular alarm, but with most alarms, you disarm the system by first turning the key in the door lock to the left and then to the right to unlock the door. Turning the key to the left first, disarms the system. Some aftermarket alarms will have a button hidden under the driver side dash that will disarm the alarm.

bought a brand new fob on e-bay with instructions on how to reprogramme

Do you have a key fob? Unlock the car with that and you should be OK. My sons Elantra is the same way, you can only get in with the fob. I guess the car thinks it's being stolen otherwise. If you don't have a fob, I'm no help