After Update, Iphone can't "find" many apps

OK, so I appreciate any help on this, but please do read this carefully, as I have tried lots of things to make this work, to no avail:
I bought an iPhone 4s and updated from my 4 by doing a backup of my 4 in itunes then restoring from backup on the 4s from that backup of my 4. Also did the IOS 5 update on the iphone 4
This is on the same computer, and with the same itunes account I have used forever
Most of my apps and songs transferred fine, but many many many others have the error "can't sync because can't find"...the apps and songs are listed in my libraries but either have exclamation points (music) or are grayed out (apps). I manually went into my phone and redownloaded them from the appstore by going to "purchased items/not on this phone" and redownloaded, so they are now ON MY PHONE.
Then I plugged my phone back in and hit "transfer purchases" (which, btw, I DID DO when I backed up my old phone in the first place..) and they are STILL not found! Even though they are ON my phone!
So just to investigate, I got to the app store from itunes and choose one of the "missing" apps. It won't even LET me redownload it from there, because it says "downloaded" instead of "buy!" so it KNOWS I have bought it, and it is ON my phone, and it still says it can't find it!!!! Help! Argh!
I called Apple's tech support and the guy just went on and on assuming I had not hit "transfer purchases' or that I had used a different account and would not believe that what I have stated above really happened! Very frustrating! Because now I know if I actually sync my phone the apps and songs will disappear and I'll have to manually redownload them from my phone again.
Hope someone has some insight. Thanks!

Please note that the old bluetooth stack will be removed during the first installer run.
Ensure that you install the new Bluetooth stack with the second run.
Check what the installer reports on the according windows in order to see if the installation was completed successfully.

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