Sounds like the same thing that happened to me. I was advised by some pretty creditable people to use one of the following: some steel wool (very fine), or scotch bright pad (very fine), or even just a good chamber brush. I put some very fine steel wool around my chamber brush and used some G96 to lubricate. I then just put it on the end of a solid pistol cleaning rod, and turned it around in side the chamber for about 3 minutes. If you have a good rod with out a handle you could put it in a drill and use a low speed for about 30 seconds.
I was told to do it for 30 seconds, but when I did it by hand it worked just fine. Took a bit longer but the problem was solved. Latter the guy who sold me the upper took a look at it and did some of the same just to be sure. Good customer service.
Good luck, and I hope that helps.