Quoted:
The bolt was pulled from a functioning rifle. It's the chamber on the barrel. I'll probably end up sending it back and waiting 6 months to get a replacement.
That narrows it down but you should try another bolt or two to be safe. If those still don't work then it's not so much the chamber as it is either the barrel extension is mis machined or the threads on the breech end of the barrel are too long.
If it's the extension you're pretty screwed a it would take a bucket of extensions to find another one that will time up correctly.
If it's the barrel threads then a skilled smith can remove the extension, re cut the rear of the barrel to the proper dimension and set the thread distance so that the extension times up again; the latter is the same principle as setting back the barrel on a bolt gun.
You said you could send it back to the maker, so you know the maker?