I also reload .40 S&W, and I ran into exactly the same problem. I had a SW99 in .40 S&W, and after firing in this gun the brass would not fit into the case guage. Even worse, if it was accidently run through another .40 S&W, it would stick in the chamber. I called Smith and Wesson, and even sent the gun back to them, and their response was that they didn't care what my problem with reloads were, it would work fine with factory ammo.
I traded this gun away and got a Beretta Brigadier Elite in .40 S&W, which has no such problem with the same and even higher pressure reloads. I think that the chamber on the SW99 was just a hair oversize, or else it was unsupported (?)... Whatever the exact reason, changing to the Beretta was my solution.