This issue was fixed for version 4.0, officially released on 14th of January 2011. Fix details are as follows:
1. All new templates in the system have the same default permissions: everyone can view, backend users can edit (also if the template is created by uploading a master page).
2. If the user has no permissions for a template, they can still see/edit a page based on the template.
Do you still have the problem using the latest build? If so, could you please provide additional information about your case?
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