ITunes is messing up my app folders.

Hi,
I have had the misfortune of having had my iPhone 4 replaced 3 times since purchase on launch day. Before each occasion I have always backed up my iPhone before going to the apple store. When I have got home with the replacement phone I have connected it to iTunes to activate it. Then I opt to restore from back up and select the latest back up. iTunes for some reason only replaces my contacts and alters other basic settings but does not reload my music or apps. In iTunes when I click on iPhone then Apps then 'Sync Apps' it loads all my apps back onto my phone but it does not put them into folders how I arranged them and I have to spend an hour sorting everything out. What is the point of a back up if this does not work?
I'm having yet another problem with this replacement handset and the only thing stopping me from having it swapped by apple is the hassle I will have restoring my phone. I have opened iTunes, clicked on iPhone and then Apps only to find that the 'Sync Apps' check box has unchecked itself at some point. When I check the box it asks me if I want to sync apps and I said yes and then selected the apps I wanted to sync. iTunes then, in effect removed all my apps from my phone and reinstalled them, not in folders like I had them. Why does it do this? Is there something I'm not doing properly?
If I have to have this phone replaced them I am going to book an iPhone and a Mac genius appointment side by side at my local apple store and explain to them whats happening and see if they can suggest a way to stop it happening. I will then restore my iPhone whilst in the store and if it places my apps all over the place then I won't leave until one of their members of staff has spent an hour putting my apps into folders.

 

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