Apply apps, causes "Cancelling sync"
I experienced that after updating apps or when adding new apps, they often can't be applied and more worse, since I updated from iOS 5.0.1 to 5.1, most of the pro-audio apps that were ok before, can't be applied anymore. FWIW iBooks is one of those borked apps, I dunno if it's because I updated iOS or iBooks.
Check iBooks > Apply >
"Syncing "Administrator's iPad" (Step 4 of 4)
Copying 1 of 1: iBooks"
Very soon nothing happens anymore and after a while
"Syncing "Administrator's iPad"
I'm running iTunes 10.5.3.3 on Windows XP pro SP 2 on Linux VirtualBox.