Help needed reprogramming keys after new vacuum pump

Looking for a little help reprogramming my keys.

In brief...both my keys stopped working a while ago and after sporadic interior light / alarm / central locking issues I found that the offside boot well was filled with water and blew the old pump...replaced pump and all was well again...other than the keys fobs.

I've gone through all the forums and tried a multitude of different ways of reprogramming the keys (key in ignition / lock door with other key / press buttons / repeat / repeat / etc etc) but with no success. Beginning to wonder if the fobs are knackered. Changed both sets of batteries but to no avail.

Is the only real option to take the car / fobs to the stealers?

Yup, was about to give that a try in the morning but then the next part of the saga started.

The alarm just went off @ 22:30, but wouldn't go off even when I put the key in the ignition (Since changing the vacuum pump and using the key in the door only opens the drivers door. If I don't put the key in the ignition within circa 20sec the alarm then goes off. When I put the key in the ignition all the doors then open / the alarm goes off)

Car started fine with alarm still going off...I had to drive around for 5 mins before it eventually stopped (thinking about my neighbours at this time of the evening!) I don't have a full VAG-com kit but one of the Foxwell scanners with full access to most of the codes and functions. The fault code on module 35 is 01374 which relates to Terminal 15:

• Anti-Theft Alarm triggered by switching Ignition ON (Terminal 15) without deactivating Alarm first

Come to think of it, the immobiliser has never worked since I've had the car in that the car always starts even when the alarm is going on.

I'm truly at a lose now....

UPDATE

Thanks for the offer aragorn...I'll be in touch if I'm at my wits end...shouldn't take too long if this continues!

Yes, the indicators do flash when the alarm goes off...I'm confident it's not a faulty siren. Scanning the system after an activation reveals the alarm was triggered by the interior sensors and then Terminal 15 after I insert the key in the ignition so my logic tells me the alarm system is functioning as designed.

So I've only had time to delete the key fobs from the memory via my foxwell unit. I'm not 100% it worked as the module numbering / descriptions on the foxwell unit is a little different from Ross-Tech. in saying that I suspect that because (I think) I've now wiped the keys from the memory the alarm stays on for several minutes before stopping. I've not yet figured out how to stop it...it just gives up after a few minutes of driving!

Incidentally I can now lock all the doors / boot without setting the alarm via the lock/unlock button if I press this just as I close the door. If I use the key in the door, the alarm sets.

I'll hopefully give the key programming / matching steps a go this weekend when back home. Incidentally is there any other way I can test both fobs are actually working without going through the matching process?