After opening ChipScope Pro Analyzer and removing all signals from the wave window, I see some of these signals again when adding a new ".cdc" file and dropping signals from it to the wave window. This happens when I move the last signal added to the wave window.
The work around for this issue is to select another signal in the wave window before moving the last signal added. After selecting a different signal, you can then move the last signal added to the wave window. This issue will be fixed in ChipScope 10.0.