I have the same problem. I noticed that even though I've uncovered all the map areas, there a blank line on the achievement as if there was another unnamed area or something and that seems to prevent the achievemente for being completed.
On another subject how did you complete the Makeb explorer achievement? I've explored everything but I won't get it either and there's not blank line.
Before I uncovered Bugtown, I had "Farnell Research Facility" on the list (in gray). It was the last one I needed to complete the achievement. After I uncovered Bugtown area, it disapeared, lefting a blank line instead. Never showed up checked (in green).
I had no problems in Makeb.