Ok guys I will try keep this one short.
I have a ba mark 2 turbo xr6 ute. The ignition column fell apart so I purchased a second hand one. Installed it is got one key with it I it bought an aftermarket key with chip and had the key cut. Had a mate come over within scan tool to program it all up. It had heaps of error codes that would clear so we determined the bcm was buggered I got a new one else and installed it. Okay we tried again this bcm communicated properly. Here's where the frustration happened everytime we tried to program keys it wouldn't let us and when we tried to crank all that would happen is the alarm would go off everytime with code theft detected and smartshield flashing on dash. After much swearing we decided to take the alarm out. The alarm was now fully disconnected and removed. Tried reprogramming same thing happened wouldn't crank smartshield light flashing with code theft detected . I can here the starter relay under dash clicking and we also get the electrical sound that sounds like it goes to the ecu under bonnet. We tried again disconnected battery for 15 mins. this time a weird thing happened we got a single quick crank then nothing smartshield flashing they detected code again. I am at the point of giving up as I can't think of anything else. And yes the battery was fully charged. Any help would be great.

I think you need to do a parameter reset when installing a new BCM

Yeah pretty sure we did that on the scanner it countdowns 10 mins on the scanner to clear everything.