this is a bug; i will try to fix in next version.
The way it works now is it tries to check your start menu "Startup" group.
If it finds itself there, it checks the box, if not the box is unchecked.
When you check the box it adds itself to start menu "Startup" group.
SO, if your seeing the box checked each time you start it, it means its somehow not removing itself from your start menu "Startup" group the way it should be. for now you can just delete the shortcut manually fromt he startup group in start menu.