Did you measure the outside diameter of the case? It seems you were very thorough on length measuring but didn't see this, or missed it.
I had this issue with new brass one time in a rifle. Since it was unloaded new brass, I just ran through my sizing die and the tough to close bolt problem went away. This was a number of years ago, and I think it was Winchester brass but can recall for certain.
Since the resizing die seemed to fix the issue for you, something in the original sizing must be off slightly would be what i would lead to, just pinpointing may be tough.