A lot of people have already gave you the answers, but I'll offer a suggestion: Each time you find a dungeon, go onto your overview map and insert your own label with some kind of numerical indication (eg Dungeon 1, Dungeon 2, etc). They seem to survive despite the black map problems, that is you can still see your blue flags on top of the remasked areas. At least you'll know which ones you've already done. Once you do so, you can even go back onto the overview map and remove the old tags and replace them with "done" as you knock each one off.
Ralph