Ok, I checked the alignment and it's fine. I realigned the .38 special sizing die with a piece virgin brass.
I loaded some virgin brass, and no bulge at the bass. I'm on my way to the range, so I'll post the results.
But, since a 9mm case is wider at the base than a .38 short colt case, if I fire a short colt in a 9mm chamber, won't I see a bulge?