One of the cases has a long scratch on it. The scratch can be seen in the picture of one case being extracted from the chamber. That makes me wonder if there isn't something in the chamber that is dragging on the case and scratching it. My suggestion is as above, polish the chamber. Also, thoroughly inspect it for burrs or debris.
The case neck deformations are probably being caused by them striking the aftermarket top cover (soft brass meeting hard steel with force).