Maybe its the immobilser...although a " ball ache" its worth a try if all else fails TJ.
I disabled the immobiliser in my 2000 LDV Convoy after similar problem.
It has the 2.5 non turbo diesel engine known as the banana engine made by ford. Don't know if this works on other models but Here is how I did it...
1 Remove the anti-tamper plate on the back of the fuel pump. This is hard to do. You have to remove the 13mm bolts holding the plate to the fuel pump and the bolts holding the plate to the engine block, as well as the mount. Then there are 5 bolts holding the plate by the injector pipes. On mine one of these was hex and the others were torx (star) heads. You can leave the 13mm in the centre of the injector pipe assay as this is part of the fuel pump and not the anti-tamper plate. You will have to disconnect the injector pipes to remove the released plate. I found by disconnecting the first 2 pipes i was able to squeeze the plate out behind the other 2. You will also need to remove the solenoid control module on the back of the pump to expose the fuel stop solenoid.
2 Well done if you got this far nearly trucking again now. Connect the fuel stop solenoid to a switched 12v live. I put my switch in on the dash.
3 Pull out the ashtray. Under that is the immobiliser control unit. Next to the unit is the starter inhibitor relay. This may be yellow, green etc. but is always beside the immobiliser control unit not the two relays beside the fuse box. You should pull out the relay and jump the double red and white wires to the double red and white wires via a fuse. I used a fifteen amp which does the trick nicely.
4 Turn on your new fuel stop switch and then start the van on the key as usual.
Note: This disables the immobiliser making it redundant. It will flash all manner of patterns after this fix but is out of circuit. The van will now only turn off on the new switch and although the electrics are disabled when the ignition is switched off the engine will run, even without the keys once started, until the switch for the solenoid is turned off.