I have a virtually identical problem. Originally I could set the alarm using both the key in the lock and remotely. However the drivers side stopped working with the key. The remote stuff was fine, but opening the car from the driver's side with the key in the lock did not disengage the alarm. However it was also intermittent. So sometimes when unlocking with the key in the lock, well, annoying... and noisy.
The passenger side worked fine using the remote or with the key in the lock :roll:
I did notice that if the physical key unlock had not disengaged the alarm, then the boot would not open. In this state, if I then physically opened a door, the alarm would pop. A kind if litmus test if you will!
It was in a Ford garage for an unrelated reason a while back and I asked if they could a have a look. They said they'd fixed "loose wiring", and it worked perfectly... for about three months before going back to the above.
Fast forward a couple of years and the problem seems to have changed yet again. I got in the car one morning and noticed the clock was wrong. Unbeknown to me, the clock was correct, just some of the LCD bars had stopped displaying. I put this down to some kind of mechanical/electrical stroke
Now I am unable to disengage the alarm or drop the deadlocks using the key in either the driver or passenger side lock. It does lock, yes, but no deadlocks.
I keep meaning to have a look at the wiring but meh
Good luck!