This warning message is generated if QuarkXPress notices that, at the end of diary generation, the generated output file contains more than one layer.
The cause for this message could be one of the following:
•You are using a Layer Token but at the same time, you used the Remove OPF Layers setting in the current script's Diary Generation Options (in which case another message should have been issued along with the present message).
•The removal of layers from the template(s) which are used by the current script failed (in which case another message should have been issued along with the present message).
In most cases, the extra layer is empty and causes no problems. If this message represents a real problem, please send the script to technical support.