Updated apps on devices not syncing back to itunes library?

Before the questionable "upgrade" to iTunes 11, I had no problems when I would update apps directly on one of my devices, and whenever it later synced to my iTunes on my MBP, it would automatically update those apps in the library. I have two iPads, one iPhone 5, and an iPod Touch 5th Gen. So, for example, I could update apps on my iPad 3, and when I synced it to my MBP, iTunes would update the files in its library. Then, when another device synced, it would get the updated app. No need to download individually to every device from the App store.

Ever since the iTunes 11 upgrade, though, this no longer works. All I did was update, made no changes. But I can update apps on my iPad, sync it to my MBP, and the apps aren't updated on the MBP anymore. So when I sync the other devices, they don't get the changes. If I do the updates from within iTunes, it'll go out to all the devices when they sync still, but the updates on the devices are NOT updating the itunes library even when synced now.

I don't know if there's another new setting somewhere that I'm missing that has to be checked now for this to happen, I've been looking around and don't see anything that seems to apply.

I'm not even going to go into the flakey WiFi sync issues where it's totally random whether it'll see any of the devices or not until I go through random power cycles on them - another "feature" I never had problems with in iTunes 10... I'd almost revert back to 10 except there ARE some features I do like with 11...

Thanks for any ideas or help.