Do you sync your iPod Touch to that same computer? I'd bet any amount of money you do.
Not that this is an excuse, because I agree it's broken, but I never have this problem with my iPhones and ALWAYS with my iPads. It seems that iTunes doesn't deal with multiple iOS devices very well and always mucks up the process.
Apple definitely needs to fix this.
PS: That's why I just call it a day when I lose an iPad. I NEVER sync apps on my iPad to iTunes any more; just music and tv shows and such. Everything else, I do OTA. Yes, it's a pain in the ass when I have to 'start over' but I'd rather deal with that than the syncing drama.
It's definitely a broken experience, which is surprising because Apple really is good with UX stuff.
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Current Apple Stuff: 24" iMac, iPhone 4, AppleTV (original), 4gb Shuffle, 64gb iPad 2.
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