Apps bought before 3.0 upgrade are synced but don't show up

After I upgraded to iPhone OS 3.0 (I also upgraded to iTunes 8.2 just before that) all of the apps I bought/downloaded (priced and free apps) before the upgrade except two (about 33 apps) will sync to my iphone. Itunes shows the information at the top that it syncs it.
BUT when the sync is finished the apps are not on my homescreen (except for 2 apps) and they're not visible in spotlight search or whatever it's called that's to the left of the homescreen. Apps I bought after the upgrade work fine however. In settings>general>about it displays all the apps being on the phone and the same with the memory bar and info in itunes - it shows that the apps are on my phone.
I tried to erase apps from itunes and the phone and buy them again (download them for free because I had payed once). That didn't make any difference. I then tried with deleting the apps off my phone and buying them from itunes store directly on the phone. What happened was that an app would be downloaded and the installation would start but then it froze in that state. I said "installing" and there was the bar and the bar had gone all the way to the right end where it froze. The icon wiggled if I held down any icon for some time the way you do when you're gonna rearrange the homescreen. But there was no cross on the corner so I couldn't delete it, and I couldn't open it. If I rebooted the device or installed a completely new app bought in the itunes store on the phone this frozen icon saying "installing" would disappear. I waited pretty long before I did any of that to see if the app would finish installing. Then afterwards I checked settings>general>about and there it showed as if the apps were on the device.
Another issue I had in connection with this is that I kept getting the message in iTunes that my computer was no longer authourized or something like that. But the thing is it has been showing that same message for a long time and it always asks me if I want to authorize it, I click authorize just to get the message that my computer or account or what it was (sorry, forgot) already is authorized and then the sync will proceed as it should. This thing about the authorization is weird because it is authorized.
I also tried with restoring the phone but it didn't help. I tried with reinstalling iTunes and that didn't help either.
If anyone else has had the same problem I'm grateful for advice, help, comments or anything.

I lost several App Icons after install of 3.0 upgrade. Facebook, Tweetie, Birdhouse and a few others are no longer on the home screen, but they do sync through iTunes and I can access them if I move the home screen to the right (to show the spotlight search screen) and I can open them, the icons just won't show up. It is very inconvenient, hope Apple creates a fix for this soon.

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EtreCheck version: 2.1.5 (108)
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Apps bought before 3.0 upgrade are synced but don't show up

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