What scanner are you using? If it has  timed PATS, you go into the module that immobilizer is in and there is a 10 minute security access wait. If it is coded PATS you need to have a LSID to get  PIN # or get it from dealer to get into immobilizer. The IM508 or IM608 should be able to pull most PIN s.

I am having the same problem on my 07 ford fusion and I am using the autel maxicom mk808b

 I have the same problem and also have the mk808bt that is supposed to be able to erase all previous keys and program new keys and you have to have 2 keys that I do,,,, I access the security of the 2009 Ford Fusion se after a 10 minute wait period it says it was successful and I am in the security, then I click to erase the previous keys and I get a message that it had disconnected. I did this 3 times with no success. How do I contact tech support I have sent 2 emails to support @ autel.com  last week but have not received a reply

I have tried reprogramming pats keys before with maxisys ms906bt unfortunately it didn't work the programming options are there in the scanner however they don't work, I used the ford ids and vcm and I programmed the keys no problem, when you contact autel they ask you for the log file, you provide the log file to them, they don't do anything with it, sometimes this $2000 dollar autel scanners are just paper weights, they claim to do the functions like pcm coding and it doesn't work do your self a favor and try the $200 dollar clone vcm, it worked for me.