Update...
Thanks Lobitz, fixed it last night. I thought the same a ground disconnected or a battery problem.. Turns out the I needed to clear all faults stored in the computer and I found a bad positive connection within the smaller fuse box attached to the positive battery terminal in the engine bay, it houses the PCM fuse, funny thing is.. This second.. Smaller fuse box isn't even in the engine bay diagram for my 2.0 crd diesel in the manual! Isn't supposed to exist! Any way I was going to just order a new fuse box (it's about 4 inch by 2") but before that took all fuses and relays out and stripped it and put it back together and seems fine.
Lesson learnt.. Never let the AGM battery go flat at a body shop either, the booster pack they used caused lots of faults to be store which may have immobilised the alarm. I got told by an auto spark to always take the battery off and charge off the car.. Easier said than done when you have to take the wheel off though, so people tend to take the easy option and jump it. Not good with a redtop battery, also now know you should use a certain charger suitable for AGM's. As it's happens I have a couple of oxford oximisers for my motorbikes which are suitable so result!
Thanks for the reply!!