Hi,
I found the solution for this problem somewhere else I can't remember where because I read so many posts and tried so many things.
I don't know what criteria Apple iTunes 11 is using to sync apps with iphone and ipad, but I don't think it is only with updated apps. I downloaded an app I didn't have in my iTunes Library, used it for a while, then updated it through Appstore in the iphone, and it was synced with iTunes...
Well, to transferr ALL your apps from iPhone or iPad to your iTunes Library do the following:
1. Conect your device to iTunes.
2. Click on the iPhone or iPad once it appears on the left.
(My iTunes is in Portuguese, so I don't know if the translation will be accurate, but I think it'll do)
3. Go to File > Devices > Transfers purchases from "name of your device"...
It'll start transfering all apps from your iPhone or iPad to your iTunes Library!