I never clean primer pockets on pistol ammo and never have a problem with primers not seating properly. Many others have the same experience.
I won't tell anyone not to clean them. It can't hurt, and if it makes them feel warm & fuzzy, then do it.
It sounds like an adjustment problem, or like someone has posted already, an occasional tight pocket.
I tumble, run the clean cases through my progressive with nothing but the sizer, prime with my RCBS hand primer, run them through my progressive with the expander, seater, and crimp die. My progressive dumps powder in the 3rd station through a drop tube with 2 brass "funnels". One works with .32 and smaller and one fits .35 and up.
IMHO a hand primer can do a better job than a progressive setup for consistent priming, but I have limited experience here. I do know it is better than using my progressive to prime.