Darren,
I've been reading this thread from time to time and skimmed through it pretty quickly, so forgive me if I'm repeating something that has been stated already. Having said that, is your UT guy using more than one angle wedge to look at these indications and from different sides of the weld where possible? I ask this because with the thickness you have, you should be able to verify pretty quickly the location provided the UT guy is figuring using his Sound Path correctly(trig). By using more than one angle and trying to remain in the first leg, he should be able to nail down the location very accurately. If he isn't completely sure where his sound is and using his trig correctly he could be seeing an indication and marking it on one side when it really is closer to the back side or visa-versa(been there and done that, bought the T-shirt :-) ). I too, commend you for looking into this as deeply as you have. There is a reason for what you are seeing(or not seeing) so i wouldn't give up until you solve your questions. Obviously indications do not move around unless it was interpeted incorrectly the first time or the welder put something back in(chances of it being deposited in the same spot are remote, but...). Not having the whole situation sitting in front of me(UT machine, UT tech, weld example, ect...) if is purely a bunch of guessing going on here, but most of us UT guys and welders have made mistakes that sound very familiar to what you are experiencing.
BTW, I would look hard at that sub-arc set-up before doing too many of these joints, if it is giving you guys that much trouble to keep the deposited material clean.
Gotta run...looking forward to reading more about your situation.