Unfortunately, some dungeons never turn up as 'cleared' even if everything is done the way it's supposed. (Bosses defeated, associated quests completed, artifacts found, etc..)
While I don't have an answer, I'd like to post a related question. Is it normal for the dwemer ruins around Blackreach and the great lifts to have their doors reset, and does this have anything to do with the cleared flag? The first time I did the three dungeons, I snuck past the centurions, the dungeon wasn't marked as "cleared", and its shortcut door was closed when I came back there (didn't know about the great lift at the time). Furthermore, the actual entrance into Blackreach gets reset as well, so when I tried to re-enter Alftand from below, I ran into a wall.
The weirdest thing though, is that I got Raldbthar
and its Great Lift to appear as "cleared", but couldn't get Alftand to be cleared. In fact, I found that Alftand was 'cleared' for the first time when I was nowhere near the place.
Also, the great lifts tend to have their doors on the surface re-closed on a seemingly random basis. Very annoying. The doors in Blackreach itself are fine, though.