I have never had a problem with this but I almost always use CD's that have a solid white surface. The text below is from Sharpie's website...
Is the SHARPIE marker safe for writing on CD's?
Sanford has used SHARPIE markers on CDs for years and we have never experienced a problem. We do not believe that the SHARPIE ink can affect these CDs, however we have not performed any long-term laboratory testing to verify this. We have spoken to many major CD manufacturers about this issue. They use the SHARPIE markers on CDs internally as well, and do not believe that the SHARPIE ink will cause any harm to their products.