I don't recall this error or problem.
Try resetting the preferences again. Create a project; add a menu. Save. Close. Does that project open?
How are you opening an existing project? Are you selecting a .ncor file and opening that? Do you open Encore, then select the existing project from the drop down list? Or does Encore not open that far?
How are you opening Encore without opening a project? From a shortcut on the desktop? From Start -> Programs?