I'm sure this answer is too late to help the poster but I had a similar problem and had trouble finding an answer on the internet, but my mate fixed it so I thought I'd share the solution we (he) found!
Basically, I changed the battery and this armed the immobiliser. I don't have a key fob so had no way of disarming it. Had no code number to input into drivers door so rang the original dealer who gave it to me. Tried inputting it a number of times to no avail. It didn't even feel like what I was doing was being registerd in any way. My mate had the idea of taking the door apart (prising off the inside panel, after having unscrewed the door and window handle) to check that the central locking system was connected properly to the immobiliser. It wasn't. So, upon connecting that back together, we were able to input the code and disarm the immobiliser. Trouble was, when the door was shut and locked, then reopened, the immobiliser kicked in again. Turns out that some bright spark had the idea of allowing the key to arm the immobiliser but not disarm it, which explained why the previous owner had disconected the wire from lock to immobiliser. So, we reconnected, disarmed the immobiliser, and then disconnected again, and, no more problems.
Hope that's of some help to someone.