At least I think the noise is coming from the crank. Ever since I had to replace the tube in my back tire it's been sounding odd. For one I couldn't perfectly fit my back tire on. The side of the axle with the crank fit well into the frame's notch but the other side wouldn't go in all the way -- if that is at all specific enough imagery.
Anyway, whenever I pedal now the crank makes an odd scratching noise when I pedal down. It's less noticable at higher gears.