That is the classic symptom of an ECU that is not associated with the alarm ECU. I have had this when having my ECU reprogrammed by Z and F Tuning. When I first fitted one of the racing ZR Cup ECUs I tried it and had exactly the same problems you had. It was not until Mark had connected his lap top and reprogrammed it so that they recognised each other did it work.
I dont know if it is possible for the 2 to get 'de-programmed' and I regulary leave mine with the battery disconnected for weeks with no problems. Might be worth a quick call/email to them though as they may be able to help out?