There are additional ruins to explore outside of the one you enter for the mage guild quest. One is a maze that nets you a dragon shout, another is the room where you would go to put all the dragon priest masks you found on altars.
There's a mound outside between the entrances to the maze and the dungeon, kinda looks like a barrow's entrance. Inside, you will find a skeleton leaning against a wall with some face carvings, the skeleton has an orcish dagger plunged into its chest. That's where you get the wooden mask - and since you said you got 2 masks in that area I'm assuming one of them was the wooden mask. If you want the details on the masks, just google "Skyrim wooden mask" and you'll find your way to the wiki entry, which probably contains minor spoilers.
If you do have all of this stuff done, I don't know what to tell you about why it's not showing as "cleared". I'll have to check when I'm in-game again to see if mine says it or not.
Just checked out mask room and cleared still didnt appear. How many floors does Shalidor's maze have? I have cleared the one with 4 staffs and dremor fight. I checked map and there is one more entrance to it through south-east of the map but I have no clue how to get there.