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I want to leave the desktop locked while using VNC to connect to a remote Windows machine.

Normally I believe when you VNC and unlock the desktop the physical server's desktop is also unlocked. I don't want that.

Anyway to prevent it?

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RealVNC can do that. I haven't checked other VNC distributions.

From VNC Server Free Edition 4.1 for Windows :

Disable local inputs while server is in use


The mouse and keyboard physically attached to the server computer can be disabled for the duration of a remote connection, preventing local users from interacting with the computer.


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