Here is the [url=http://www.ar15.com/forums/topic.html?b=3&f=4&t=165221&w=searchPop]Thread[/url] for others, including my self, with the same problems.
I have a J&T flattop upper with a M-4 profile barrel with an ARMS #40 BUIS. To sight the thing in, the #40 had to be cranked all the way to the left (front sight tower leaning left). So after purchasing the appropriate tools; barrel nut wrench, action vise block, etc... I had to disassemble the upper. Once the barrel nut was loose, the barrel would rotate counter-clockwise (as looking at the muzzle) a good 1/8". I used the peening meathod to fill the space so the alignment pin wouldn't rotate back when the nut was tightened back. Well, I'm going to have to file a little off of the one side to make it perfect. Right now the #40 is about half way between center and full left. I'd like it a little better...
If it was new, I would send it back to J&T, but I got it off of the EE second hand, but almost new.
Good luck!