I gave cleaning the areas with what I presumed to be scratches from the dock a try to no avail. The smudges from the rubber pads are gone, but the scratches remain. They're thin little things, looks almost like hair. I tried like hell to take pictures of the scratches to share, but they only show up in the right light, and my cell phone camera can't seem to catch them.
I'm going to try expanding the clearance on the dock by leaving a SNES cartridge wedged in there for the next day or two. I snapped a picture of the measurement before the cart was in and after the cart is in (I had to brighten the photo with Photoshop). It's a decent amount of expansion, like 1/16 of an inch...
I'll report back if it makes any difference. I'm kind of expecting the dock to just pop right back to its pre-widening size when i take the cart out, but we'll see.