I learned that if Quark ask for editing these character sets, that these characters exist in your document. Sometimes when I copy text from a PDF and paste it into XPress, some characters get in some strange way emulated, which is not visible at the first look. To check this, go to the usage dialogue and look for some strange fonts in the used fonts list. Klick on show... You get pointed to the location of the font problem. Remove it with your standard font or style and/or edit the emulated type. After searching and removing of all appearances of the strange font, the message is gone forever. I would be happy about some feedback.
MacPro 12 Core 2,93 GHz, 32 GB RAM, Radeon 5870, 6 TB HD, XPress 9.2, CS5, LR 3