GMs really have no idea what they're talking about when it comes to the goblin/bloodsail rep part of this achievement.
It's LIKELY that you only need to be Exalted with the factions at one point in time.
However, Achievements reparsed on the 4.0.3a release as far as I know. If you had 39/40 on "The Exalted" and 4 of those were Goblin reps you trashed for Bloodsail, the reparse would set you to 35/40. They did this to reset the new achievements they added to the Quest category. This is just my theory, but it seems to fit based on the QQ around the date of that patch about 'losing reps'.