I'm putting together a Specialized Hard Rock I picked up; it was rather badly neglected.

There was a large area on the left chainstay where the paint was gone. I inspected it as carefully as I could, and could not see any sign of bending or cracking. Considering how poorly the bike had been treated, I just figured the previous owner had let the tire or wheel get misaligned or..... Something.
After Dremel-ing off all the surface rust I repainted the area with model-making enamel and went to install a pair of nice new 2.1" tires. The rear one rubs on this spot.

Pulled everything off again and measured everything carefully, there does not appear to be any misalignment and the tire center lines up exactly with the frame. However, the right chainstay is strongly indented.... The left one is not. The tube is full diameter as you can see here:



Is this normal? Dunno why they'd provide tire clearance on one side and not the other..... I might have to just use different tires for this, but it does look odd.
(thought I did a pretty good job of paint-matching, BTW)