Weird. I say that because, this has definitely happened to me before, but never figured out how to repeat it or make it happen on purpose, always reboot again and its blank desktop for me. But I 100% sure have had settings panel appear already open after reboot on occasion too.
This is very weird. I have never faced this issue before. Actually I have no idea how to make it start after boot. Something is bad. The only idea is reseting bodhi profile or erasing hidden .e folder in home folder.
Check the following setting. Click the icon in the upper-left corner of the Options panel. Open window > remember property. Open advanced properties. Navigate to the "Options" tab. Look at the last check box: "Start this program on login" If this is checked, it will start automatically when you log in.