Vehicle immobilsed/wont crank unless 20 pin diagnostic connector left disconnected.

I was asked to look at this for a trade customer. It had been parked up for quite a while as the owner is in the forces. When he came to use the car, apparently the battery was flat & after charging it wouldn't crank/start.The owner bought a new key & still couldn't get it to crank. When I got it the battery was flat. After charging the battery, I scanned all control units using Autodiagnos connected to the 16 pin J1962 socket, but only got communication with the engine control unit. After getting communication with the engine ecu, I assumed that the vehicle was probably not immobilised, so tried cranking with switch wire to starter & it started & ran ok. Trying to start via the ignition switch, the starter would attempt to turn when the key was turned quickly, almost as if the immobiliser was a bit delayed in preventing cranking. I then checked for a 20 pin diagnostic connector & scanned all units again, when I managed to communicate with all units, cleared all faults, then found that the central locking would work via the remote & the car would start via the ignition switch as normal.I parked the car up & thought that it must have been just a case of clearing the faults & re-initialising the key, but when I came to start it again, I found it was the same as before(with the bbus sounding as before, when the door was opened). I then found that the central locking and starting was ok if the 20 pin diagnostic connector was left off. when pins 20 & 14 were being linked with the lid, the cental locking wouldn't work. Pin 14 is the battery feed & pin 20 the txd from various control units.I have previously enquired about the purpose of linking these pins before & was told that it was to prevent any false triggering/communication to the control units, holding the txd(diagnostic line) line at battery voltage. Since the car has been parked today, the bbus decided to sound again & then stopped after a few times.(hopefully it won't go off tonight)
The customer has decided to leave the diagnostic connector lid disconnected for now, but if the alarm goes of randomly then, i'll have to disconnect the bbus again.
I have the vehicle for a few more days yet & would like to know what could be causing the problem, but at the moment can't spare the time to look in to it further & have yet got to mot the vehicle.
Sorry for the long post, Kind regards, Andrew