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Root Trouble changing themes on Liberty 2

I recently switched over to Liberty 2 and I like to change my themes up pretty often. However, it seems that every time I change themes it is like I am flashing a whole new ROM in that I have to restore all of my apps and set up my email accounts again. Is this normal with Liberty 2? I remember when I was on Liberty 1.5 I could change themes and all my apps, icons and email accounts would be the same. Am I doing something wrong here?
 

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