Hi mate the immobiliser stops the fuel pump and the spark /ignition the engine will still turn over the immobiliser is built into the ecu that is what makes me think that you must have chipped keys have had this problem be for on a late mk5a as near the model change to mk6 some did have the pats system fitted to them
Near the ecu in the passenger footwell the is a test plug try a code reader of get a ford dealer to see what fault shows up the one i know about had a faulty key reader on the ignition lock this was replaced and the codes rest by ford and it was ok as for removing the immobiliser ask ford or a ecu specialist hope this is of some help to you