How are you launching the configuration tool? Try using the configuration tool link located at:
Start->All Programs->Microsoft patterns & practices->Enterprise Library 5.0 Silverlight Integration Pack->Enterprise Library Configuration->EntLib Config for Silverlight
This will use the Silverlight specific profile.
Or if you launch from within Visual Studio using "Edit Enterprise Library V5 Configuration" it should give all of the configuration types (desktop and Silverlight).
Enterprise Library support engineer