restore doesnt restore apps

Hi

I am probably missing something really obvious here, but if i restore my iPhone i lose all my apps, music, photos.....everything. I have to manually sync them all again.

To give more details. I have had an issue since 6.0.2 firmware was released that the App Store shows on my phone that updates are available, but i can never get it to load the page to start the downloads. I click on the App Store to be greeted with a blank screen, even though it tells me i have 3, 4, 10 updates needed.

I have tried to update them via my PC using iTunes, but it only updates them on my PC, not the phone.

So, i deceided to restore the phone and see if that helped, before coming on here to ask advise.

I backed up my phone to iCloud as usual, then performed a 'transfer purchases' in iTunes, then a backup.

Once that was completed, i restore the phone. It installed the latest software, rebooted, then asked my complete a restore via iTunes.

Once the phone was back up and working, i only have the standard 20 apps installed, no music and no photos. It has given me my backgrounds and contacts though.

If i look in iTunes, all the apps are there. Its forgot all my music sync options and my photo sync options as well.

I can of course, rebuild it from iTunes, but yet again (i had this same issue when i upgraded from my iPhone 4 to the 5) i am going to have spend the next hour or so regrouping all my apps and putting them back on the correct pages (yes, i have mild OCD)

For the future, what am i doing wrong please? Why does it not remember my installed apps and their layout please?

Thanks in advance.