Sorry to hear you had problems, Gunner. I know you were excited about shooting it last weekend. As you know, I have an original - a Burnside Contract - not a repro, so I don't have the right extractor, but if you shot two flawless sets of shells through her in the first stage, then I would guess that the problem is not with the magazine tube, but with the operator

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One likely cause would be overall cartridge length. In the .56-50, if a cartridge isn't just right - if it's either too short or too long - the sucker will hang up and jam. Remember what happened to me one year at Blue Mt.? I know it's possible that some of the lube from bullets can get into the seater die on your reloader - at least that happens to me with the cheap .45 bullets I shoot in .45 Colt - and then your rounds start coming out marginally shorter. It really doesn't matter much in a revolver, but it certainly could in the Spencer.
Perhaps if you make up some dummy rounds to OAL specs and then cycle them through the gun at home, you could see how they feed, first slowly, and then at speed. If they work flawlessly, then you know it's the ammo you used on those stages, not the gun. If they work sometimes, but not others, then it's either the gun or the way you're working the lever (which ultimately comes down to the gun as well, but may or may not be fixable). It may be that you feed the rounds smoothly when you work the lever slowly, but do something different when you get excited.
If you really want to get into this, have Deadeye Donna run videotape of the breech/action as you "shoot" the dummy rounds both slowly and fast. Then you can watch (and if necessary frame-by-frame) the shells as they come out of the magazine and get levered into the breech. That's pretty involved, however, and might be a heck of a lot of trouble.
Good luck with it, and if it fails, I'll trade you sight unseen for my cheapo o/u derringer...
