iTunes won't restore home screen arrangement from backup

I backed-up my device to my MacBook Pro at the Apple Store right before I got my replacement iPhone. I did it with an empty iTunes, as my library was on an external drive that I didn't have with me. I don't sync my device to my Mac often (probably did it a month ago). The genius told me that it will still work and I will get all my Apps back. When I got back, several times I tried to restore it from Backup and get all the apps and app layout that I had on my old iPhone. I failed every single time. I then made sure that the iTunes library had all the Apps that I had on my iPhone and had them all up to date; this was about 200 apps I had to download or update. I then erased my iPhone and got ready to restore it again. However when my iPhone came back up it didn't restore all the apps and app layout that I had on my iPhone at the Apple Store. The apps & layout was old by several weeks. However at one point the correct home screen arrangement in iTunes at one point.

iTunes will back up the following information (from Apple Support):

• App Store Application data including in-app purchases (except the Application itself, its tmp and Caches folder).
• Application settings, preferences, and data, including documents.
• Home screen arrangement.
• ...

Thus restoring from my backup should give me the correct home screen arrangement and application data. The iTunes Library file (because I have all applications downloaded and up to date) will add the Application itself. However for some reason my backup file is not restoring the correct home screen arrangement (restoring weeks old arrangement), even though all the other data that is on it (ie. pictures I took the day before) is restored.

I have moved my Device Backup file to another computer's Guest account, plugged in my external device and tried restoring it from that computer's Guest account to see if it will work correctly from there. Once it the device was rebooting I removed it from iTunes. It had no apps on it. I reconnected it to iTunes and then it showed the correct home screen arrangement for about a minute until it started syncing, and then it reverted to the old home screen arrangement. I now deleted the other backup files so that the only backup file is the correct one. After doing this I restored it again and once again I see the correct home screen arrangement until it starts syncing. I want to have it restored with the correct layout so that I get the Application data for the new applications that are only present on the correct layhome screen arrangementut.

The correct home screen arrangement is present until after the "preparing apps to sync" and then it reverts to the old home screen arrangement. I'm guessing it is syncing to the old preferences overwriting the correct home screen arrangement. I only want it to restore with the applications and not sync. Also with the correct home screen arrangement in iTunes if I drag App A onto App B it creates a folder with two App As. Then when I close the folder App B is only present. I have something really weird going on here! The incorrect home screen arrangement also shows page 8 being grayed out even though their are apps on page 9 and 10.

With the only backup file (the April 19th one) I tried it again. I click restore from backup and left it plugged in. After it rebooted the apps in the iTunes view was the old home screen arrangement again. I removed the iPhone after about 3 applications synced. I then replugged in the device and the correct home screen arrangement was shown again. I deleted an app from the correct home screen arrangement and clicked apply. After a few seconds it reverted to the old home screen arrangement again. What is wrong with iTunes? I feel like I need to delete some file somewhere.

I have currently been erasing the device from the device settings. I am now going to try clicking restore from iTunes and I will try again restoring from backup.

How can I have it restore the backup version of the home screen arrangement and not sync the home screen arrangement on iTunes??