In an up to date 11.10 the Cairo-Dock icons gradually become blue ? circle icons after a few hours or days after restart. The launchers still work when clicked, but they become harder to identify as more and more of them "forget" their original icon. Any workarounds to periodically refresh the dock or fixes?
Right click on Cairo Dock>Configure, then click on the "Appearance" tab, then try selecting a different theme for icons. If the question marks go away, then it must be a problem with the theme you were using. If that doesn't solve the problem, then you could try choose the correct icon manually for each icon that isn't working. However, to me, it seems strange that you say they fade, or something.... Anyway, hopefully it'll work.