You dont understand core of the problem. (please do excuse me Im not trying to be rude, EN is not my native language - I dont know how to express that sentence without being rude, but be sure that I dont have that intention)
Problem is happening to files that ware created outside of Paint.net. In test image, I provided in zip file, in my first post - you can observe bug happening.
-First open native file in PS or Gimp and see resolution - 72
-Than open in Paint.net and check there - 96
-Than save image in Paint.net without resizing it or doing anything - just "save a