I use PADS9.3.1 version. You have to set your port symbols in Setup>Settings>Special Components. And set correct port symbol name in Tools>Cross Reference> Modify Cross References Settings. Also check Setup>Settings>Display>Xref Annotation.
There are technotes explaining scout in supportnet:
-Setting Up and Running Cross Reference - The Basics (iCDB):
- Cross-Referencing a Design - For PADS Flow
- xrefs are not appearing in my design: