ITunes not updating iDevices on Sync

Just bought a new iMac and decided it was time for a clean start so I didn't import my old prefs, etc w/ Migration Assistant. Instead I just did a drag and drop with all my data files, including the iTunes Folder and Mobile Applications Folder. I then updated about 100 apps via iTunes and tried to sync my iDevices. The backup seemed to happen, but none of the apps were updated. However, if I went to my Apps section in iTunes with the iDevice plugged in I could hit a button on the respective app to manually update at next sync.
So bottom line: iTunes won't automatically update  all apps on iDevice at sync, but I can manually update individual ones.
I've never experienced this before, but I'm not that versed on iTunes 11 either. Am I missing a setting somewhere? The only one I see is to automatically download NEW apps, which isn't my problem here.
All devices are using the current version of iOS 6.

Same here.  I have to search for and manually hit the update button on each one to get them to sync.

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