you can fix this properly by speaking to Abacus car alarms (google them). They know the meta alarm system in the alfa well and can reprogramm your unit and send you 2 new fobs and a key card for 100 quid.
If you only have 1 key fod, no backup fob and no key card. I would recomend you do this, rather than just look to get you one remaining fob working again.
regarding your problem though I do remember when I changed the battery on my fob I had a similiar problem. A dealership fixed it by doubling up the battery (putting 2 of those penny batterys ontop of each other) and by also giving the infra red bit on the fob a damn good clean) they didnt charge me for doing this.
Does the fob work if you use it like right next to the dector (near the central reversing mirror thing)
Cup Number 99