I am having the same problem. I have looked at dozens of sites with infor and none of them seem to alleviate my problem.
Im at 66%, and im nearly positive that central boston is the only one im missing (evidenced by the fact that i have all the stuff he wanted in my inventory). There was a point in the game where he showed up, but when i went to drop off the supplies, he dissapeared when i got within minimap range (ive had this happen before, it disappears at the edge and then reappears when the minimap picks them up) but it didnt reappear. I was busy so i didnt really think anything of it,as normally they reappear soon after and now he hasnt returned.
Ive searched the general area that sites have pointed me too VERY thoroughly. If anyone could post a picture of the dude standing where he stands, i could match the picture up with an exact location in game (not on the map). Its a lot to ask, and i dont really expect anyone to do it, but until that picture pops up, there isnt enough info for me or apparently the OP to go off of.
Extra kick in the nuts: my DNA sych has rounded up to 100%. But 100% isnt quite 100% now is it.