I've had a similar issue with my new Uberti Flattop Target .44-40. Like you said, some of my black powder handloads would not cycle all the way around. I did some research and found out about the recoil shield "shelf" on Uberti's that is sometimes too abrupt and needs to be smoothed out. I filed it a little bit but that didn't help. My mistake. The real problem was I wasn't seating my primers all the way. I was using one of those Lee loaders where you hammer the primers in and I just wasn't seating them right. I switched to an RCBS Automatic Priming Tool and that solved the problem.