Went through Fort Greymoor and killed all the bandits and looted everything i wanted too... made sure i went into all rooms and the dungeon still won't list as cleared... any ideas?

I just cleared out a Fort myself, but it won't mark it as cleared on my map either.

There could be an area in the fort that is accessed by a quest. Dustman's Cairn is this way for example. If you go in there before taking one of the quests from the companions it's smaller than it really is, because the dungeon has a secret access related to the quest.

Ah, I see. Thanks.