Quite a late answer but here is how to fix it:
https://superuser.com/questions/1864078/need-process-explorer-to-start-minimized-at-startup
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I'm currently using Process Explorer 17.02.
Normally it could be started into System Tray by using command line parameter '/t'.
This was working on older versions perfectly.
After switching to 17.02 Process Explorer starts allways with full window, whether with or without parameter '/t'.
Quite a late answer but here is how to fix it:
https://superuser.com/questions/1864078/need-process-explorer-to-start-minimized-at-startup
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Handy namaste I am in a while ago and I am not sure if