If permissions of site was changing after deploying through Visual Studio 2012, please follow the instructions below -
1. Go to [My Project] -> Properties -> Publish Profiles -> [My Profile] – Web Deploy.pubxml
2. Add line “<IncludeSetACLProviderOnDestination>False</IncludeSetACLProviderOnDestination>”
3. To the Property Group element
This should stop VS 2010 from altering permissions.
For Visual Studio 2010, please see here
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