This happens when you've activated "add pc drives at startup" and save the config after pressing F12. "Add pc drives" adds the drives to the list, so saving them will save all drives into the config file. Next time the config is loaded "add pc drives" adds the drives again, so you have everything twice.
Either save the config only from the startup window or remove all hard drive entries before saving from the F12 window.
Bye,
Thomas