Phantom PCM

[M31]

Recently had the factory PCM on my 2002 Boxster replaced with an after market Pioneer touch screen GPS/ipod unit. The old PCM used out of date CD ROM's from 2001 that I just couldn't find updates for so I gave up and replaced the whole works but...now when I activate the factory alarm system it's acting a bit strange. A double horn sounds after the lights blink twice. Page 27 of my owners manual says this is a fault indication. Page 26 says when the alarm is armed the following areas are monitored: Doors, Front and rear Lids, Convertible top lock, radio, storage tray between seats, passenger compartment.
The alarm system worked fine immediately before the upgrade. The Porsche tech who installed the aftermarket GPS suspects that the car is "looking" for the PCM...well guess what...it's never going to find it! Has anyone else out there been through this and have a remedy? Everything locks the way it should it's just now my car sounds like every other car in the mall parking lot instead of stealth like it used to.