I'm going to echo Benjamin here. While not a 6×47L, I had a very similar experience with 223 Lapua brass fired in another rifle. I full length sized them with the intention to fireform to 223 AI, and they sent me into some head scratching time to figure it out. The base was too large. The bolt would almost close but would not cam all the way down. As soon as I marked the cases all the way down to the base with a good black stripe, it was obvious. And yes I use a Co-Ax for all of my smokeless reloading.
While it's possible the problem is in the neck area, I bet it's the base. As someone else mentioned, try some new cases. I suspect they will chamber after being necked down.
FWIW, I also load 6×47L and started with new cases. The cases last so long, I figured I would wear the barrel out before the cases.
By all means, let us know what the issue was.