ITunes removes new iPhone apps every sync

I occasionally install a few apps directly from the iPhone's app store while I'm out traveling with my iPhone.
When I get back to my Macbook laptop and sync, though, iTunes removes every single app I added.
Fo example, I added AmericanExpress and WalMart on my iPhone last night. When I get back to my laptop and sync this morning, AmericanExpress and WalMart are removed form my iPhone! The apps are in iTunes, and I can re-sync them back to the iPhone, but it's very frustrating to have to take a snapshot of my iPhone every single time before I sync so I can see what apps are removed.
I have SYNC APPS checked and AUTOMATICALLY SYNC NEW APPS in iTunes.
I erased my iPhone and started from scratch (no RESTORE) last week and the same thing still happens.
Is the iTunes app corrupt? Is there a preference I can remove to see if iTunes is the problem?

UPDATE : After trying the user ID login/logout on the iPhone and iTunes, I went to UTILITIES > GENERAL > RESET > RESET ALL SETTINGS on the iPhone.
After the iPhone restarted, I got the animated new iPhone intro and selected "set up as new phone". After pressing NEXT, I was brought back to the iPhone as it was before the RESET. (Nothing was erased, despite the "set up as new iphone" selection.) The wallpapers had changed, and I had to re-sign in to GameCenter and the local WiFi on startup, but all the apps were still there.
I downloaded a free app on the iPhone directly again. (Cut The Rope Holiday GIft). I plugged the iPhone in to the MacBook, went to iTunes, and pressed SYNC.
Cut The Rope Holiday GIft was removed from the iPhone.

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