Aww, poor guy. I'd just keep things positive & not make a big deal over it. If he gets 'weird' about some boundary & is hesitant, just allow him to explore at his own pace & comfort level. Don't push him, or try to force him to 'get over it', but also don't make a big deal or fuss a lot about it/him either.
It would be nice if they could talk & tell us what their past experiences have been, but regardless of what has happened in the past, all you can do is support and work with the dog in front of you today. He'll probably* get over it once he realizes that scary things don't happen in those situations any more (if they ever did?)
* One of my dogs is 11 years old, adopted at the age of 7 months. He came to us with a LONG laundry list of phobias, one of which was crossing through physical thresholds like doorways. He has, for the most part, gotten over this, but! To this day he has to circle two or three times to get his courage up in order to bolt through the 5' wide opening in between our kitchen & sun room. He sometimes gets "stuck" in there & we have to remind him "The force field's down, it's safe to come through!" (sigh... dogs are weird!)
It would be nice if they could talk & tell us what their past experiences have been, but regardless of what has happened in the past, all you can do is support and work with the dog in front of you today. He'll probably* get over it once he realizes that scary things don't happen in those situations any more (if they ever did?)
* One of my dogs is 11 years old, adopted at the age of 7 months. He came to us with a LONG laundry list of phobias, one of which was crossing through physical thresholds like doorways. He has, for the most part, gotten over this, but! To this day he has to circle two or three times to get his courage up in order to bolt through the 5' wide opening in between our kitchen & sun room. He sometimes gets "stuck" in there & we have to remind him "The force field's down, it's safe to come through!" (sigh... dogs are weird!)