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Can I make another account on my Windows Machine but with totally different configuration? eg. different startup programs, all services switched to manual on different accounts etc..

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Services are system-level (specific to the computer), not user-level (specific to the current user). –  Ƭᴇcʜιᴇ007 Mar 29 '12 at 16:07

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This may not be the most elegant solution, but if you remove startup items from the startup for all users (via msconfig), you can add shortcuts to the wanted items back to the startup folder in the start menu on a per-user basis. The startup folder is found in

%appdata%\Microsoft\Windows\Start Menu\Programs\Startup
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