Hello there i have the same problem, i use mac, now maybe more details could help us, when i connect my iPad air 2 with ios9 to iTunes, i go inside iTunes to apps where it shows the ones installed inside the my iPad, but none appear on the upper column, the screen shots shows the app, and below my app with data to transfer in between the mac and the iPad appear, so when i go to transfer purchases manually it obviously won't do it, it start and in 1 sec its finished, its like it could not even see any apps installed to be transferred.
So i checked my iPhone 5 with iOS 8.4.3 and it does show up all correctly and even it does make the transfer, i have the same id in all, and even updated to OS X el capitan with the latest iTunes, so its a problem on the iPad, now of an easy solution i would put it on dfu mode and force the restore, but i have apps for design and my designs are inside and the apps are not the problem but the info inside, now also iCloud is fantastic as long as you have a decent internet speed connection, but i live outside of the city and believe me i can't depend on a backup from iCloud, on windows with windows 7 on a pc and the last iTunes it happens the same, so what could be the problem.
