How to start System Explorer minimized (in tray)

Start System Explorer with parameter "/tray".

If you want to start System Explorer minimized in tray automatically after user login, then chek option Menu>Options>Automatically Start After Login.

For version 2.0 or higher:
If your System Explorer starts after login in NOT MINIMIZED state, then please open System>Startups section and delete item with value name "SystemExplorer". There will stay item "SystemExplorerAutoStart" and all should work on next login as expected.