I use Starline brass which reportedly is a little more robust than other brands.
I was surprised to find that I was having a hard time with the separate crimp. Ammo was not chambering properly. I reset the RCBS #3 to crimp the case mouth and whaddya know-it works.
Were you loading Black Powder? Years ago a friend was having trouble with his Black Powder 45 Colt loads. He was seating and crimping in two separated steps. He was also putting a wad in on top of the powder, I'm not quite sure why. Anyway, it turns out that with his full load of Black Powder, plus the wad in there he was compressing the dickens out of the powder. He reloads on a Dillon progressive press. In the few seconds it took for him to work the lever to rotate the shell plate for the next round, before his rounds rose up to be crimped, the over compression of the powder caused his bullets to rise up a bit so they were getting crimped with an Overall Length that was too long for his rifle. I forget now if he got rid of the wad inside, or reduced his powder charge, but anyway, when he reduced the column of powder inside the case the bullets stopped rising up and his problem went away.
So were you loading with BP?
I used to load 44-40 with Winchester brass. The brass at the case mouth was ever so slightly thinner than the brass at the case mouth of Starline brass. This would work out well if somebody needed to use 'fat' bullets in their ammo. Technically, the rifling groove diameter of 44-40 should be .427, but a lot of manufacturers are using the same .429 barrels that they use for 44 Special/44 Magnum firearms. Following standard logic, a lead bullet should be about .001 oversize of groove diameter. So the proper bullet for a .429 barrel could be as large as .430 in diameter. Uberti rifles tend to have tight chambers. So a .430 bullet might expand the case mouth enough that the finished round was difficult to chamber in a tight chamber. That extra .001 or so of 'thinness' at the case mouth in Winchester brass could make the difference in that situation.
Unfortunately, it was sometimes hard to find Winchester 44-40 brass, they only made it a few times per year. So I changed over to Starline brass because it was always available. Ever so slightly thicker at the case mouth, but not enough to make a difference in my 44-40 rifles.
I just checked and 44-40 brass is back ordered at Starline. Firs time I have ever seen that, it was always in stock when I needed some.
Hopefully they will catch up with their orders soon.