After resetting devices apps don't sync between iTunes and devices

I use Windows iTunes 11.0.1.12 in Windows 8 together with an iPad 3 w/ 6.1 and an iPhone 4S w/ 6.1.1.
As my app collection grew too much I decided it was time to start over from scratch. So I deleted all apps within the iTunes library and reseted my devices, telling them to be configured as New Device when the question was asked whether I wanted to use a backup of the device. Then for a while I downloaded apps to the devices directly on the devices without using iTunes.
All seemed to be nice until I connected the iPhone to the computer to sync it, mainly for backing up the apps on the devices. But this is not happening. I can sync as often as I like, apps which I downloaded on the devices are not copied to iTunes' library when I sync the device. Likewise apps that I obtained within iTunes are not copied to the devices when I sync.
Does anybody know how I could fix this?

I have the exact same problem. Help!

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