I have the same problem. I have a die that should cut two 3-1/2" squares, but they are 1/4" small on one side.
I assumed it was from fabric shifting or stretching and tried all sorts of things with no luck. Finally cut a single sheet of paper, made sure the paper cuts lined up exactly with the blades (so verified that nothing shifted during the cut), and measured the paper. The DIE is definitely off!
I bought it new, but from an Etsy seller. I haven't bothered to contact Accuquilt because I assume they won't do anything about it. I checked the die at Joann's and the ones being sold new appear identical to the one I bought (same serial numbers, same graphics) so I don't think a new die will be any better. I suppose I should try Accuquilt, just to see what they say, but I am prepared to be disappointed.
My other dies are fine though. I have a 3.5x6.5 and a 1.5x3.5, and a 4.5" square and those are all precisely correct (I checked, with more paper). Just this one is bad.