I'm having a similar problem with the Explorer of Makeb achievement. All areas are checked off, but I am still able to track the achievement. However, nothing appears under the title Explorer of Makeb. I believe this issue stems from discovering Brakan Mesa last. When I entered this particular Mesa, nothing popped up on the screen stating that I have surveyed the entire map or even that I had found Brakan Mesa. I have found others with a similar problem in this thread http://www.swtor.com/community/showthread.php?t=633268. I submitted a bug report a month or two ago when I ran into this issue but it doesn't seem to be as we'll known due to the specific nature of the bug.