I just updated to iOS5 and something strange in iTunes is going on.

It says that I have 5.6 GB of "Other" in my iPhone. I don't know what this "Other" consists in.

For the update to work properly I think that you need all of the apps that were on the iPad on your computer's iTunes, otherwise it can't re-install them and therefore their content - did you do File > Transfer Purchases before updating ? If you now download them on your computer's iTunes (or if you've re-downloaded them all on your iPad then Transfer Purchases) then you could try restoring from your backup and see if you get your content back.

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