Sometimes there is a hard buildup in the chamber consisting of dried gun oils, fouling, etc. that needs to be removed. I used a brass brush and steel wool on a brass rod turned by an electric drill on the chamber of an M1 Carbine that was giving me problems and now it works perfectly. The chamber doesn't need to have a high polish but it should be smooth enough to let the case go backwards to re-seat the fired primer.
I was trying to figure out polishing the Model 99 chamber, your method gives me an idea of using a brass cleaning rod and threading a .40 cal brass brush on in the receiver, wrapping it with a bit of 0000 steel wool and using the Makita to give it a polish. It is definitely in need of it. I'm going to do a major cleaning and oiling, this will be a perfect addition. Thanks!
Oh, btw, these were factory Winchester 150 gr loads, so I'll bet the rough chamber is the culprit. It's not pitted, but it has a matte finish, so I'm betting that it's just putting a bite on the cartridge.