When you upgrade from Connect You 11 to 12, settings may wrongly remain in the export plug-ins. These are easy to remove.
Normally a PDF export style in Connect You shows the buttons "Cancel" or "Ok";
Hold the Option key while looking at the button;
"Ok" now changes to "Delete";
Click "Delete" to remove the export style.
This works when exporting a Certified PDF from Adobe InDesign.