Can you list all the checkboxes that were not selected when you do these steps:
1. Start BlackBerry Desktop Manager
2. Start Application Loader
3. Click Next until you see the list of checkboxes
4. View the list of checkboxes of installed & not-installed apps.
Or did you select all checkboxes (One or two dozen of them)?
The checkboxes that were not selected, may give a clue as to a missing module.