I'm also in a similar boat.
The first character I logged in with was my newer engineer, that I definitely have not run any dungeons on. I checked the vendor and everything was locked out.
I then checked my Necro, who was created 3569 days ago, and I have *definitely* done TA with him, as that is how I got Rabid exotic gear back in Core. I only have the achievements for explorable for TA and AC, but I have done all the story modes for all the other dungeons (for the WvW tracks). But, everything is still locked out for me, even on the Necro.
Does it have to do with the first character you log into the game with? Or maybe the last character you played on? For me in both instances it was a character that did not have any dungeons completed.
