Immobilizer issues

[DRKNITE]

I just purchased a 2001 boxter s. The drivers door locks not the passenger door with the key fob and the interior lights do not come on. Other wise the car runs really nice and I did have it checked out. The previous owner was able to secure a complete matching computer system (computer, immobilizer, alarm module, transponder, keys and of course the pill for the original key) once the parts swapped out, everything worked Central locking system, interior lights but now the car won't start. When I swapped everything back, the car ran great but the original problems.. Any way, I took it to the dealer today and they couldn't fix the problem. They claimed the car wouldn't communicate with their diagnostic system and offered no solution. I know the car was connected to a computer when it was at another mechanics place because a full systems check was done. Any thoughts? Thanks for your help