Omni: "The +0.003 diameter I referenced is as measured on cases after they have been primed but before powder and bullet seating. I think the problem is somewhere earlier in the process, like during the depriming/sizing step...."
It's impossible to 'expand' a case shoulder in an FL no matter how the die is adjusted. Nor can he expand/swell anything in a seating die that hasn't yet been used.
Omni, if you DO have an over-size shoulder you have a defective die, get it replaced. I rather suspect you have no problem with the shoulder diameter but instead have a problem with insuficient shoulder set back. Try turning your FL down another 1/8th turn and size again; see if the cases won't chamber properly then.