Migrating from iPhone 3GS to iPhone 4 * Apps disappering

I have an iPhone 3GS with OS4. Most of my apps works ok, but I some need upgrading to work properly under OS4. So I wait patently.
But I have another problem:
I have bought an iPhone4 and try to migrate from the 3GS.
But it seems that there are Apps disappering on the way, and I would like to know how to fix it.
My prosedure is like this:
Full backup of the 3GS
Recovery of the same backup to my IPhone4
.. and som of my apps are gone.
I have used hours to put stuff into my Apps and hate to lose it all..
So currently I keep on using my 3GS.. Would like to move permanently to my new phone! Hope someone can help.
PS! IT is not jailbroken.
Have the same version of OS4.02 on both phones.

After you restore from backup, you MUST sync to restore your itunes content, which is selected under the various tabs in itunes, just like you did for your 3GS. Itunes content is NOT included in the iphone backup.

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