The immobiliser chip doesn't go out of sync if the ecu and clocks are disconnected, the only thing you can have problems with is the remote part of the key.
If the ECU, clocks and key were out of the same car there should be no coding involved so it sounds like you have a mis match of components there or if you fitted the new ignition barrel the reader could be faulty
You can swap your old ignition barrel back into the car then change the lock part over to match the new key to check that out:
If it isn't the reader then you will need to code the clocks to which ever ECU you use so you will need the SKC off the new ECU or the old one and the clocks then code in the clocks and keys
Neil
