IPad 2 to iPad 2 Restore Failure - Apps all Gone

My iPad 2 screen cracked (without being dropped), and to Apple's credit, they gave me a new one yesterday at the local Apple Store. I had done a total sync on damaged iPad before going to store, and then took the new iPad 2 and plugged it into iTunes. Of course, I chose to do a restore, and it seemed to take a very long time, loading everything up.
Issue: All of my music loaded up just fine, but ZERO apps. I then looked at iTunes, and it is showing no apps for the iPad. Big problem, I have purchased what amounts easily to over $1000 worth of apps. I then figured that if I just started manually loading some apps, with the iPad not plugged in, that I would get the standard message that I have already purchased the app, so it is free. I tried this with Pages (yes, I know, I should have "tested" this theory with a .99 cents app, not so swift). It charged me!
Any ideas as to what went wrong here? How do I get my apps back?
Thanks,
Scott

Are you using the same iTunes account that you used to originally download the apps ? You should be able to re-download them for free if you are : http://support.apple.com/kb/HT2519
Also the backup contains the app contents and settings, but not the apps themselves - if you can get the apps into your computer's iTunes library then the restore should work better (in order to restore the contents of an app it needs to be able to install the app itself first)
Message was edited by: King_Penguin

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IPad 2 to iPad 2 Restore Failure - Apps all Gone

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