I'm having the same problem and it's becoming very annoying. I DL from Stardock Central, but I also bought the separate version for work. I set it up with all my submenus. It is quite slow when setting up, but otherwise it works well...until I have to shut down and reboot my PC. Then all my submenus are gone. I had to go back and recreate all my submenus, just for it to happen again. I ended up uninstalling the darn thing. Why can't they have something similar to Docks where I can save a backup and load it when it crashes? And why should it not bring back my submenus on a simple reboot?
Is someone in stardock working on this issue. I think that it is a great and very useful utility.
Thanks.