Unless I misunderstood something I think you want to use SaveAsBinary/SaveAsXml to serialize your design-time settings (before ther user changes anything), and then call the LoadFromBinary method when you want to load in the default settings. It is not necessary to call any of the control's Reset methods before loading, as the method does that before streaming in the new property values.
I think I get this now. I used the SaveAsBinary method to persist the state of the control to a stream after changing the order of some of the groups via the Navigation Pane Options dialog (I have to assume this is the menu you are referring to), and when I used LoadFromBinary to stream the object graph back in, the order was lost. This is a bug; you might want to report it as such.
[Addendum, March 5, 2009, 5PM EST] While investigating this further, I found that I probably did something silly with the stream (never reset the position) when I reported this was not funtioning correctly earlier today. Upon further inspection, it does seem to be preserving the order of the groups.
I am using the WinExplorerBar with the Outlook style. It would be nice for the user to modify the menu to its needs when he wants to, so I set SaveSettings to true to save the changes in the control.
Now the user would like to restore the default layout, like is is created when no user changes were made (=the layout I set in design mode)
How can I reset the control to the default settings at runtime?
Sorry, I am definitely not following this. If you could please clarify which menu you are referring to here, we can try to help.