Here is an article that will help you troubleshoot the App syncing issue that you are experiencing. This article is for versions of iTunes prior to iTunes 11. However, most of the information is the same. If you prefer the classic view of iTunes, I have included the commands to enable these features. To enable the Menu Bar, you can press Control-B on Windows. To enable to the Sidebar, go to View > Show Sidebar or press Control-S on Windows.
Hope that helps,