You are correct in saying that dnn does not recognize it.
To work out where the content panes are located on a skin, dnn does some trickery - basically it searchers thru the objects defined on the skin
- basically looking for any objects that are <p> <div> <td> container type objects.
the act of assigning and id=HeaderPane and runat=server to <div> actually tells the skin to create an object of class <div inside the skin object.
However, it only searches thru the skin object itself - that is it examines container objects directly on the skin
... as a result it has no understanding that it would need to drill down into your header object
looking for a <div> container buried inside it.
As a result, any <div id="HeaderPane" runat="server" ></div> needs to be on the skin itself.
And I would suggest that a custom skin object would not change where the <div id=HeaderPanel needs to be defined.
Having said that - it may be possible to create a custom skin object that could be used to directly place a editable html area in your header.
Westa
PS was actually kinda surprised the MENU provider object worked in your header.ascx container - would have thought that it may have expected a skin as its parent - but then again mmm i guess no real need for that.