If your shorter neck cases are getting more "crud" as you state, then they are not expanding enough to seal off the gases when you fire the case. It's likely that's because the case neck is too short, or your firing low end loads.

I don't know what your definition of "short" is, but if they are too short, I would consider tossing them and just trim the brass to the SAMI spec. I find, at least with the .223 brass, the easiest thing to do is just use the Lee hand trimmer. I use a small battery powered screwdriver type gizmo and simply buzz 'em down until the stop hits the holder. That way all of the brass is trimmed to the same length, and for consistent velocity, that's what you want.

FWIW

Dave