This does not occur in Windows versions later than Windows 2003.
This is not specific to WCF applications, and may occur in other applications doing similar Windows Authentication.
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When ServiceSecurityContext tries to negotiate with the client process, it utilizes the authentication package which has a reference to a stale token created during boot time. This results in the new groups being missed out.
The restart of the process/service gets the updated identity as the process does another log on with its identity and gets a new token while restarting. Hence we see the groups under System.Security.Principal.WindowsIdentity after restarting the process but not under ServiceSecurityContext.Current.WindowsIdentity.
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