I had the same problem, thanks Kanasis for your answer, it helped me to figure out what the problem was.
The Brigantine Isles were fully explored on my map as well, but remained listed as missing on my list. But there was also another area missing (Ourobore Caves), so I went to explore them and it worked.
So what Kanasis means, Gothor, is that you have to go through your achievements list and look for other areas listed as non-explored. If it’s already explored on your map, then it’s not this one which is actually missing.
That’s the list which is bugged, because some areas appear twice on it, but are marked as explored only once …