Not sure how a dead batter in a remote or VSS is going to cause the alarm to go off...
If the door latch is messed up and sending a random open door signal, then that would cause random alarms. If you have VCDS (VAG COM Diagnostic System), then you can go into the Comfort Control Module and view what the last 4 alarm triggers were to confirm this.
I've also seen where the OEM radios will cause random alarm triggers. The fun part is the radio and hood latch are wired up together for the alarm. Pulling the radio out some and reseating it tends to fix this issue.