**This issue has been resolved in ArcGIS (Desktop, Engine, Server) 9.3.1 Service Pack 2.**
The junction is not set as the default for the edge-junction rule after the following actions have been taken:
1. Establish an edge-edge connectivity rule.
2. Set the junction as the default for the edge-junction rule that was implicitly created when the edge-edge rule was established.
3. Click OK.
4. Re-open the Geometric Network Properties dialog box.