My BFR has scratch marks too so that's not that big of a deal. A little annoying when you spend so much $$$ on a guitar and the strings scratch trough to the wood, but what can you do 
My other JP6 has a nut issue like yours too except it's only on the high E string (.10 string) and it buzzes cause it lays on the first fret. Unfortunately for me I bought the guitar from a friend about 2 months after he purchased it new back in November of 08 so even though it's still in it's first year, it's a non-transferable warranty so I'm screwed there but don't get me started on that one.....
Anyways I feel your pain, good luck with customer service they really are a great team. If it is still under the first year warranty I'd take it back to my dealer and make them pay all shipping costs to have it fixed right.
My other JP6 has a nut issue like yours too except it's only on the high E string (.10 string) and it buzzes cause it lays on the first fret. Unfortunately for me I bought the guitar from a friend about 2 months after he purchased it new back in November of 08 so even though it's still in it's first year, it's a non-transferable warranty so I'm screwed there but don't get me started on that one.....
Anyways I feel your pain, good luck with customer service they really are a great team. If it is still under the first year warranty I'd take it back to my dealer and make them pay all shipping costs to have it fixed right.