Not sure what your issue could be there, but if the two boxes of ammo you ran through it were the same ammo it could just be that your barrel just doesn't like that load at all. Still though, 5 MOA groups is a bit much even if that were the case. In any event, definitely try a couple different loads as it may just be a very picky barrel. (don't know if the PRC is picky in it's own right when it comes to loads)
As for the bore being dirty, that's normal. Savage puts several rounds down through each rifle at the factory - first to proof the barrel and then later to verify function before it get a serial number and is boxed up.
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