I haven't run into it either, but I don't know maybe if it crashed or something...
You do know you can save your themes, right? Config window, "Themes" 2nd from the top of the left panel, "Save Current Dock" button at the bottom of the right panel. "Load previous dock" button right above that to re-load one you've saved.
If you had the free version installed before the Plus version, the free version does need to be uninstalled before installing the Plus. If you didn't do that, uninstall it as well after uninstalling the Plus.