Hi,
Yep, chamber throats and also chamber necks probably undersized from the factory (some early Ruger 44-40 had both problems; I had one like that, also). Send to Ruger and have them fix or replace the cylinder.
As for brass, Winchester and Starline brass best; throw everything else out. CBC/magtech and Remington the worst.
As for dies, make sure dies are setting the neck far enough back; factory ammo neck usually is set farther back than sammi spec, in my experience, just to avoid this problem.
Good caliber, especially for black powder.
One can occasionally find a spare Ruger 44 mag cylinder for sale and have it fitted to same gun; now one has a very handy conversion caliber gun; shoot 44-40, 44 mag or 44 spec (and 44 Russian!). (Ruger used the same .429 barrel for their 44-40 and 44 mag single action revolvers; 44-40 purists hated this (originally it was .427 barrel), but I think this was a great idea. Much easier to find bullets for reloading, with much wider selection.)
Don't give up on it; just get it fixed (then again, if he does give up, tell him to post it for sale here first!)
(Much, much harder to find a spare Ruger 44-40 cylinder to fit to a Ruger 44 mag gun.)