When I am in iTunes with my iPhone connected via USB, the apps tab does not allow me access from my MacBook Pro - All the apps and iPhone views are greyed out.
iTunes does Upgrade apps from the Apps Store and they are correctly stored in the iTunes Mobile Applications folder, but no upgrade to the iPhone apps.
I have checked my iPhone with iPhone Configuration Utility, and do not see anything not expected.
I cannot access the iTunes App Store from my iPhone, but can download new apps to my MacBook Pro using iTunes. The new apps do not get loaded on my iPhone.
I hope this helps in getting some knowledgable support. I do not want to restore my iPhone unless it is the last hope.