When I set up machines for a roll crimp, I back of the seating stem so it doesn't come into play. I put an sized, unflared case in the seating/roll crimp station, and with the tool head as low as it goes (not camed over) bring the die down to where the crimp section of the die just touches the mouth of the case. Then bring the die down another half turn. Then I adjust the seating stem to get the desired OAL. You will mess up a few bullets in the process, but that's jus the way it is. If you happen to have a loaded round with the correct OAL, you can put that in the seating station and with the tool head in it's lowest position, bring the seating stem down to where it stops on the bullet. This will get you pretty close but you might need to make some minor adjustments.
The condition you have happens when the crimped portion of the brass bottoms out in the crimp groove, or digs into the bullet while the bullet is still moving. The brass has nowhere else to go so it begins to buckle or bulge the case below the bullet.
This is also a common problem with bullets that have no crimp groove like 45 ACP. If people try to crimp too much they get a bulge below the bullet. Doing a Taper Crimp in a separate station alleviates the problem. For 45 ACP, I set the Seating/Role Crimp die so it removes the flair, but doesn't crimp, then crimp with a Taper crimp die.