I'd say you have 2 copies of the page existing in your site, one with a fully qualified url and one without. The one with the fully qualified url might be marked as "Include In Menu" not checked so only one appears in the menu. You can find such pages under Adminsitration > Add/Edit Pages aka PageTree.aspx
no way is mojoPortal creating duplicates especially duplicates with different properties, these pages must exist.
Hope that helps,
Joe