I don't know if this is a special circumstance that only applies to me, but I'll throw it out anyway because it worked under my conditions.
I was having the same problem after I had to reset settings on my iPad - 14 apps wouldn't transfer because it said this computer wasn't authorized, but when I authorized it it said it already was. And the apps, which worked before, wouldn't open in the iPad.
Then I remembered that sometimes when I bought an app it asked be for my iTunes account info, and sometimes my mobile me info, which iCloud was now using. I tried authorizing under that account, but still got the error.
Then I signed into the iTunes store under my iTunes account, and saw that the apps showed as available for download, meaning it didn't know I'd already bought them. I signed out, then logged in under my mobile me account, and the apps showed as downloaded.
So while I was logged into the iTunes store with my mobile me account I sync'd my iPad, and I didn't get the error message. And the apps also worked on my iPad.
So all I can suggest is if anyone having this trouble might have purchased things from iTunes under two accounts, to try syncing while signed in to the iTunes store under the other account. Hope this helps someone.