Or, looking at the pics it looks like a fair percentage of the powder is discolored and could have been something in the case which contaminated a portion of the powder. It's the primer or the powder that was the problem.
If the bullets are not the same length, you will have an inconsistent depth in the case if the overall lengths are the same. As long as all the cartridges fit in the magazine and in the chamber I would not worry about the depth of the base of the bullet in the case.
I like the small primer .45 ACP cases as I only have to get one size primer for 9mm, .45 ACP and .223/5.56. I use small rifle magnum primers and have never had a problem with them.
Try it without and if it runs without jerking etc, then you are good. If it seems to grab or jerk, then try some lube and see which seems to work the best for you.