Had PCM replaced, anti theft is flashing, No start unless I take neg off batt.

What is your question?

Hi there, I am a novice, I had trouble with my truck. It turned out to be the PCM. I had it replaced at an auto shop. They said that the PCM was flashed to my VIN, (whatever that entails) The problem now, it thinks it is being stolen. The only reason I know this is due to forums and advice from other mechanics online. I went to pick up my truck and it was fine, Until I drove home for the day and activated the alarm. I turned on the alarm with my key fob. Went back out, no start. the anti theft light is flashing rapidly..... the mechanics say there is nothing more that they can do. Or should I say they are refusing to help. They say I need to take to ford dealer. Considering I just spent two paychecks on the replacement of the PCM, I am broken hearted that they have taken advantage of me. I can only start my truck if I never ever use the alarm/ the fob (which is brand new because I thought it was the issue) or the keyless entry. Once any of those are used the truck thinks it is being stolen. That anti theft light starts flashing rapidly and it kills the start. I am asking What I should ask for? I can not afford to be bled to death of money, that I quite frankly do not have. I can get it to start again by taking the negative off the battery and waiting for 10 minutes. Reattaching it, and it starts and runs soundly. Please advise Do I need to replace egnition? Would that circumvent the problem or introduce even more. Do I need new keys? (I replaced the fob and had it done by a lock smith that deals with these things) Please keep in mind that I am a little older and had back surgery and I am limited. Takes me a while but I get it done. I am going to have to try to do it myself.