Hi Gaz,
I hope you have indeed got it sorted and the charged battery has sorted it however, (just a hunch)
Blast a few pints of screenwash through your rear screen washer and see if it does it again.
I had exactly the same problem with mine before Xmas (05 Plate A3 2.0 TDI), My alarm kept sounding randomly when i locked the car, sometimes within 10 minutes and sometimes after a couple of hours. I couldn't work out the problem straight away so i left the car unlocked in the garage for a day as i didn't have the time to see to it there and then and it seemed to sort itself out. a week or so later i had the same problem (put it in the garage again which again solved it) This problem came back a few times until i realised it only happened when i had used the rear washer.
The problem was water from the rear screen washer which (when the seal goes) leaks down the inner lining and ends up in the boot lock mechanism. There is a small connector in there which controls the alarm and boot sensor etc which due to the way it's designed catches alot of the excess washer fluid around the contacts causing them to arc and make a connection. This tells the sensor that the boot is open which in turn set's off the alarm.
I took the locking mechanism off and dried it out with a hair dryer before replacing it which worked a treat but when i dried it out i realised that the contacts inside the locking mechanism were very flimsy and corroded to hell (to the stage where they are ready for falling apart) unfortunately they are part of the locking mechanism and so i may end up having to change the whole thing in the future but hoping i won't have any more problems since getting Audi to sort the seals on the rear washer.
Short term, if you haven't the time to strip the locking mechanism etc, just take the boot lining off and unplug the plastic connector from the locking mechanism, this will stop the alarm from going off but note, Your boot is no longer alarmed if you do this.
As long as you get the seals sorted however you should be ok and even if the connector is completely corroded you could just disconnect it as long as you don't mind the fact that your boot lid will no longer be alarmed.
As i said Bud, i hope you have solved it but if not try the above.
Kyle