You may want to clean your CD tray with some alcohol or something. Spray from printer ink can buildup on various parts in a printer. I've noticed with my R200, that ink will slowly buildup on the outer rim just outside of where the disc goes. This in turn causes the ink to wipe off to the rollers in the printer that push/pull the tray and paper through. Probably because I have the diameter for printing set all the way to the outter edges, so I get a tiny bit of spray outside of the printable area, then wipe it off later.
Maybe you have some kind of ink or other buildup in the bottom of the CD tray, which is contaminating the surface on the data side while printing? Or like jucius said, clean your disc, with something reeal soft. The ink printed on the disc has virtually almost no weight, plus it's distributed across the disc anyway. I don't see how it could affect balance of the disc to much of a degree. It seems like you have some kind of contamination or slight scratches issue already mentioned. I don't really see any difference between before and after printing scans on my discs.