Try taking a little finishing compound and going over the area. Just make sure it is NOT rubbing compound, rubbing compound WILL leave scratches. What I used on mine was 3M Finishing Compound (designed to take out scratches 1000+ grit I believe), and it's barely even visible now, even in the right light.
If it makes you feel safer, just go over it with a regular car polish, which will probably accomplish the same goal.
What you are describing does sound a lot like the way mine was though. I just assumed it was something that happened on the lot, because I just recently bought my '06 and it had been sitting at a dealership for a while.