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→Skype for Business 5.5 Configuration: HKU\.DEFAULT\Software\Microsoft\Windows\CurrentVersion\Run\Skype isn;t used by Skype, created User Config section with setting to disable startup on login
===Skype for Business 5.5 System Configuration===
Adding these additional install commands into your WPKG package will modify the registry to disable automatic updates (DisableVersionCheckPolicy), disable supernodes (DisableSupernodePolicy) and disable Skype running at login by default.
<install cmd='%COMSPEC% /C reg add "HKLM\Software\Policies\Skype\Phone" /v "DisableSupernodePolicy" /d "1" /t REG_DWORD /f' />
</source>
===Skype for Business 5.5 User Configuration===
You can disable Skype from starting on login with the following command:
reg delete "HKCU\Software\Microsoft\Windows\CurrentVersion\Run" /v "Skype" /f
==Skype for Business 5.0==