This has been happening since ios 4. Basically every time I go to a new ios, (4.2.1-4.3.2 ->4.3.2) or whatever. I re setup my jb and resync all my apps, but for some eason anywhere from 10-40 of my 71 apps throw errors, adn no matter how many times i reboot both pc\device, they just dont sync.
So I have to delete them and redownload them, and its the biggest pain the world.
I dont have anything i know of jb wise that messes with the itunes syncing, so....
and before you all get pissed at me for pirating, I don't. i have nothing related to that software on my device (neither dose gf).
any help at all? This is happening for my gf now too.
I can't really diagnose this as I've never seen it happen unless (like you said) the apps were pirated. I don't see a reason why iTunes would reject syncing certain apps. I'm not accusing you or anything, I'm just saying I've never seen this issue before where no piracy was involved.
All I can think of is perhaps you should make sure your iTunes is logged in to the account you want, make sure your computer is authorized for it, make sure your app store in your phone is logged into the same account, and try again.