permissions not retained when using Save Site As Template in WSS

Hello,
Does any one know how to fix the issue with permission not retained in WSS in .NET?
I have not trying to using the "Save Site As Template" feature to new site using the site templated I created previously but new site lost all the permssions I configured for it.
Does any one have any suggestion on how to work around this issue?

Any idea or suggestion is greatly appreciated.