I have an iPhone 4s, iOS 7.1.2, plugged to my Pc. iTunes 12.1.2 is running, and I am seeing the apps in my device.
On the right of the main screen there are copies of the icons as shown in the iPhone.
On the left there are two lists of apps. The top list shows all apps. The bottom list shows the apps that can share documents (and clicking on an app one can see the stored documents for it).
I have at least one app (Foxit Reader) that shows in the bottom list and not in the top one, which is unexpected. I do not know if there are other apps in the iPhone that do not show in the top list.
Any idea of the cause, and how to solve it?
I found another problem, which I think is related to this one. See https://apple.stackexchange.com/questions/198927/itunes-backup-not-all-apps-backed-up