Many times I have heard reloaders say to be sure to use a 'firm crimp' with their 45 Colt and 44-40 reloads. In my experience, it is impossible to get a 'firm crimp' with a 44-40. The brass of a 45 Colt is much heavier at the mouth than a 44-40. Most of my 44-40 brass runs around .007 in thickness at the mouth. Most of my 45 Colt brass runs about .012 in thickness. What tends to happen with a 45 Colt case as the crimp is formed with a standard roll crimping die is the brass at the mouth curls over as it forms the roll crimp, forming a rounded profile. If the die is not adjusted absolutely perfectly, and a little bit to much crimp is formed, the brass will bite into the softer lead of the bullet, and actually mechanically lock itself into the bullet. That is what I would call a really 'firm' crimp. This is of course when using a standard seating/crimp die that seats the bullet and crimps in one step.
44-40 is a bit different. The material is really not much more than foil. It is only about .007 thick at the mouth. Using a standard seating/crimp die, the brass does not tend to form such a nice rolled crimp as a 45 Colt crimp. Instead, the material tends to 'flow' more and take the shape of the crimp groove it is flowing into. If the die is not adjusted properly, the thin brass will bottom out on the very top edge of the crimp groove, but the bullet will continue to be shoved into the case mouth. The brass is so thin it does not have enough rigidity to dig into the bullet like 45 Colt brass will. Instead, the bullet will shove the brass down with it, and the brass having nowhere else to go, it will crumple underneath the bullet as the bullet is shoved down a few thousandths. This is the crux of why some reloaders find the 44-40 difficult to reload and often resort to using a second die, one to seat the bullet, and a second to crimp the brass radially, namely the Lee Factory Crimp Die. But still, there is really no such thing as a 'firm' crimp with 44-40. The cartridge is either crimped or it's not. If you try to give it more crimp, you will usually wind up crumpling the neck.
This is a long, roundabout way of saying, that factories are going to experience the same thing. The thin brass of 44-40 is only capable of so much holding power, you will never find the same massive crimp on 44-40 as you will 45 Colt.
These days I only load 44-40 with Black Powder. One of the advantages of loading Black Powder that nobody mentions very much is that when you fill up the case with powder and compress it with a bullet, you've actually made a plug of powder that prevents the bullet from being set back in the case, like you describe. With Smokeless loads, it is only the crimp holding the bullet there, there is plenty of air space and no 'plug'. I make up dummy 44-40 rounds that have no powder in them, just a spent primer and a crimped bullet. I use them for various things, one of which is testing the feed of my rifles when I have been doing a little bit of 'smithing'. I have found that although the bullets stay in place when run once or twice through my rifles, if I completely compress the magazine spring by loading 10 or 12 into the tube, I cannot run those dummies through the rifle more than a few times. Without the powder helping the crimp to hold them in place, after a few times through the rifle, the bullets start setting back, sometimes completely telescoping into the case. Then I have to replace them.
I suspect it is the same with loaded factory Smokeless ammo. The crimp is probably fine if you take them out of the box, and just run them through the action once, but I'll bet if you cycle them through a few times, you will see them start to get set back.