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There are known issues with a persistent disk not working if the user already has a profile on the c:\ drive. if your missing common information from your profile after a recompose I would verify where the profile is actually being stored.
There are also some third party applications that allow for user installed applications. You can look at liquidware labs http://www.liquidwarelabs.com/solutions/flexapp.asp and Unidesk although unidesk is an entire solution.