ITunes copying same songs and apps every sync

Every single time I sync my iPhone 4s (iOS 6) to iTunes 11 (OS 10.6.8) it copies the same songs and apps to my iTunes. Like right now it says "Syncing Danielle's iPhone (Step 5 of 5)" and right below that "Copying 8 of 10: MC3" (which stands for the app, Modern Combat 3). No more than 5 minutes ago I was syncing my iPhone and it was copying that app (it takes forever too because it's a big file). All I changed was adding some calendar events on my macbook in iCal then I wanted to sync it again real quick and it's copying all of these files again that it just did.
One of the problems could be that I have it removed from my iPhone but it's still checkmarked in iTunes? I can't see how that would be practical though. I would think that if I deleted a song on my iPhone, or deleted an app, that when it connected to iTunes next it would make a note that I don't want it on my phone anymore. Anyone know the source of the issue?

Some other program is interfering with itunes saving its database file.
iTunes Library.itl
This is really common for Sony Vaio users running Vista. Either disable the Vaio's music service program (VCFw.exe), or uninstall it, as Evert Yntema chose to do.
See this post
http://discussions.apple.com/thread.jspa?messageID=8545376&#8545376
And for folks who don't have a Vaio, the next biggest culprit is security or backup software scanning the itunes folders. You need to configure
Norton/Symantec
McAfee
Kaspersky
ESET NOD
IObits
Windows Live OneCare
Carbonit
Mozy
or whatever software you've got installed to ignore the itunes folder or specifically, that ITL file.
If you're getting tons of TMP files, something is interfering with itunes saving the ITL file. A workaround is to same that ITL file to a different folder or USB drive just before you close itunes.

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