Like others, I have resized 30-06 cases to many other cases. Only had your problem with one rifle. It had a custom chamber. Factory cases fit fine. I had to grind a bunch off the bottom of the sizer die, to let the shoulder portion come down further on the 30-06 case. Still leaves the sizer OK for standard cases. As noted, brass spring back is apparently causing your problem, so you need a little more latitude in your sizing. Hope this helps.
Jeff
NRA Life