I was able to complete the desert except for like two or three quests. There's a good 4-5 more quests than required there to get the achievement.I have a similar problem in Aliki'r. I think some of the 'pointer' quests that just tell you to go to the main quest giver actually counts to the number. Hence if you find the quest before the pointer, you won't be able to do the pointer and hence won't be able to get the achievement.
Same Quest Achievements in Stormhaven never unlocked for me, I hope it gets fixed soon and we get these Achieves.43/53, will be 44/53 with instance. There is absolutely no way there are 53 quests in this map. Also, my Stormhaven quests are bugged. Never got the achievement for them.
Did you do all the solo/public dungeons? as there's sometimes quests in those that you may have missed. I have managed all the achievements upto now and am doing that very area now.