I have also experienced this same weird phenomenon.
Went to Japan for a week, came back to a Flat Battery ... got the Brera going again, did the customary window reset etc, drove over to my girlfriends then came to lock the car ... no beep no flash, but alarm led flashing on drivers door.
Now ... I get 2 flashes (no beep) if I pop the boot before unlocking it and (I just tested this out of interest) If I sit in the car and arm it, then open the door ... I get the beep (continuous) from the alarm with the indicators on (continuous) no siren.
I've tried resetting everything, I've tried arming the car with doors boot and bonnet open, to try and create a fault, but all to no avail ??
Maybe we should start a thread where people state their symptons and people have to guess which country their alarm has defaulted to ??
1999 156 2.5 V6 Sport Pack 3 (190)
2004 GT 1.9 JTDm (150)
2007 Brera 2.4 JTDm SV (200)
2011 Guilietta 1.4 TB Multiair (170)
1970 VW T2 Early Bay (50)