From your description, it sounds like there is an issue with the timing.
Yes, the Carrier Block should start up before the Breach Block (bolt) is all the way back. The carrier block should NOT hit the bolt on the way up. Also to feed correctly, there has to be a small bevel cut into the front side of the back wall of the mortice the carrier rides in. If you'll visit Pioneer Gunworks site, there is an excellent set of pictures showing the fix for this problem.
You don't mention whose SS kit is in the gun, but that is important information to resolve the timing issue as well as the caliber.
Coffinmaker