The only thing I can think of is that there is an electrical problem that is keeping auto lock/unlock from working. Are the door lock switches and manual lock buttons working as they should? Are all the door lock actuators and tailgate actuator locking and unlocking properly? Any transmission troubles? (The range switch on the transmission tells the car's computer what gear you are in.) Ignition switch working properly? Any blown fuses?
Beyond that, I would just advise trying programming again. I struggled to program remotes for the Accord, only to find out I was skipping a step. (And I'd done this a few times in the past! I'm at the age now where the brain farts are coming on more often than I'd like.)
There are two modes for auto-locking--when the gear selector is moved out of Park (called Park Lock), or when the vehicle exceeds 9 MPH (Drive Lock). There are two auto-unlock modes--one unlocks when you return the shifter to Park (Park Unlock), or the other is when you move the ignition switch from the on/run position (Ignition Switch Unlock). It can also be disabled...but it seems you have a handle on that one. ?
If anyone's curious (and for future reference), here are the manual pages for the procedure:
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