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There are home screen issues with the jailbreak, mostly icons moving around, the springboard crashing, etc. I know you aren't jailbroken, but most jailbreak issues carry on from original iOS issues to begin with which is why I brought it up.
iTunes depends on a few files to read the device and show the information. When it can't find something, like the .plist for the icon layout on the home screen, that would explain the blank area. It most likely is a permission issue.
And when you have an issue like that, it's most likely that your backups will have the same problem too. So a total reset is better.
The small Over-The-Air updates will cause minor issues like this.
That is just my educated guess.
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