Join Date: Mar 2005
Location: Philadelphia, PA
Bikes: Jamis Aurora
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Keep an eye on it, if it changes in size, color, or shape, get it checked by a dermatologist, could be skin cancer.
Rust (even from inside) would almost certainly disturb the smoothness of the finish if it became a visible mark. I'd suspect a paint defect of some sort. Are you certain it doesn't wash off? It could be you ran over some oil/solvent/etc that splashed up and discolored the finish.
The easy way to be sure would be scrape the paint off down to bare metal, find out what it is, and repaint. However if you're the kinda guy who NOTICED a spot that small on the bottom of your chainstay, you're probably sensitive about the finish and wouldn't want a ghetto-looking paint job.
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Now living in the land of the cheesesteak.
But working at a job where I can't surf BikeForums all day any more...