Ok, I figured out what the problem was. Yesterday I made a hard save of my 100% playthrough, then started a new game and rushed through the main storyline so I could grab that damned achievement I missed the first time through for going through the red door on the Matt Miller mission. The stats screen was pulling info from that autosave rather than my hard save.
My first time through I was thinking the two doors would end up being another case of where you had to do it both ways to get the achievement, like how you had to do two playthroughs for keeping / blowing up the Syndicate headquarters in SR3 to get the two separate achievements. I really hate how SR3&4 don't let you rewatch cutscenes and replay storyline missions like you could in SR2.