I had similar problem. New or updated apps downloaded using iTunes 11 would not sync to my iPad during a sync operation. In addition, I could not rearrange apps in iTunes and sync those changes to the iPad. Sync appeared to run, but no changes were ever commited to the device.
I was able to resolve these problems without a full restore by deleting two apps that had inadvertently been installed on my iPad using another family member's iTunes account instead of mine.
Here is how I came to this solution. Your mileage may vary:
When I first installed iTunes, none of my apps showed up at all on the iPad "Apps" tab in iTunes. I took the advice of other threads and exposed the sidebar by selecting View, show Sidebar so I could see my iPad listed under Devices. I then right-clicked the iPad icon under Devices and selected "Transfer Purchases" to copy apps from my iPad to iTunes. However, I noticed two apps would not transfer. The error message said I was not authorized to run them on this computer. Initially I ignored that message, since it simply said they would not be transferred.
After hours of reading this forum, consulting Mr. Google, and trying other generally useless advice, I deleted both of these apps from my iPad and instantly, the app sync began to work. I had 28 updated apps pending in iTunes and they immediately synced to the iPad. I could also rearrange apps in iTunes and they would change on the iPad after running sync.
By the way, I have the box checked that says "Automatically install new apps", since I want anything I update in iTunes to be deployed to my iPad next time I sync.
Good luck and I hope this helps others as frustrated as I was.