The problems you are now experiencing could be one of 2 things:
water ingress into the alarm unit
failing central convenience control unit
The former is a possibility only because you had water in the boot and it is located very near there (actually below and behind the offside rear light cluster).
I would suspect the latter though. These units are known to fail and as they control not only the central locking, but the alarm too, it would be my first culprit. A VAG scan would possibly shed some more light.
Cheers,
Mike