Rem0o
disabling start at logon deletes configuration and plugins
I had to try something and thought i could turn of Start at user logon temporarily. But when i started FC my saved configuration was deleted and the plugin folder was empty. I had to completely start from scratch to enable FC again.
Are you sure you just don't have multiple installations of FanControl and the one you opened after was just untouched? FanControl can't delete it's whole folder like that.
I double checked, i have only one folder containing fancontrol. I know exactly the name i used for the config and it is gone (did full harddisk search).
Well there is just no deleting function of any kind in FanControl. It can't just self-clear itself, I checked to be sure but I just don't see how that's possible from the code POV. There has to be an explanation as to what happened in your case with some manipulation, but I can pretty much guarantee the program itself didn't do that to itself.
The only thing I can think of is that your start with user task had a "start in" folder, which fancontrol saved its stuff in there, and when you open FanControl directly, it uses its own folder. There might be a "plugin" and "configurations" folder somewhere on your PC.
Well, i have no idea what happened then. As far as i know i have no tasks or anything like that nor any other folders with configs. I guess it remains a mystery. Thank you for thinking with me though.