I think you've just uncovered your problem and I know whats up.

A common technique to attempt to bypass the pats is to cut the 4 wires to the receiver on the barrel and then do some other things that I wont discuss as it compromises peoples car security.

Basically it does one of two things. Ot either bypasses the PATS allowing the car to be bumped off and nicked or option 2 it screws the ECU up. I think you may be looking at a new ECU fella and then recoding your keys to match.

One port of call before you do get an ecu.. Check the ignition switch for damage.

Sorry I'm not bringing good news. Repairing Scrote damage is always a pain!