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i'm not seeing how i just do a simple normal back up like i normally do thru itunes. i can't just do it the normal way if my phone is jailbroken, then go and restore that back up later to my phone even if its not jailbroken
 
You can still do a normal backup if it is jailbroken.

If you want to save your Cydia apps, download PkgBackup in Cydia.
 
why are not all of my back ups showing up in itunes??
Sync your apps to itunes.

Did you use Installous to download some of them? iTunes recognizes if they are hacked apps because they are paid apps that not on your iTunes account.
 
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