I had this same problem. It was the extractor...it was good you smoothed the extractor tooth some but did you also sand the channel as well? Also, after doing this I had to change the OEM extractor spring to a +25% extractor spring and I now over 8k rounds through my CZ with no issues whatsoever.
I would look again at the tooth and slightly profile it...800 grit sandpaper is what I used and made sure it was very little at a time.
This issue was more prevelant in my reloads then factory ammo...I think its because reload brass had some nicks and scratches on the back end of the brass that the extractor would get caught on.