I have two keyfobs, I put fresh batteries in them -- this issue is so strange - if I have both of the keys with me in the car, after I take one key out of the ignition one of the keys (its random) will operate the door locks, but not both of them right away - after a minute or so, both of them begin to function just fine.
I tried to find programming instructions for the 2012 MKZ, but it doesn't seem to have done anything. The owners manual says you can insert one key, wait 3 seconds, take the key out, put in a second key (like you are programming a third key) and it's supposed to program the IKT as well... that did nothing. - I did find the procedure where you cycle the key on and off 8x ending in the on position - the door locks did cycle like they were supposed to per the instructions, however, pressing a button on either of my remotes just causes the horn to honk once, not cycle the door locks to indicate that programming for that remote was successful. Taking the key out of the ignition at that point just leaves me where I started - but remotes work after a minute or so, and my dads Ford remote still locks and unlocks my doors. I tried my brothers Ford remote - it did not respond at all. So it seems like an issue with just his remote being programmed as an extra somehow?
Maybe I'm not doing the procedure right, but if anybody else has any ideas on how to program the keyfobs, let me know.