I'm having the same issue, but it's not just on system shutdown. If you "close" the app, it just closes the window. It's still in memory so it just recreates the UI when you reopen it. But if you close the app and end the two OneCommander processes ("OneCommander" and "OneCommander Dialog Connector") it exhibits the same behavior.
This is incredibly irritating in that I maintain two panes with a list of tabs for my workflow, which includes accessing these folders on a regular basis. On every reboot, I end up having to manually open tabs and put them in the proper order for my muscle memory.