An update on this old issue with corrupted footers in WF3 (a corrupted footer does not allow feature reordering). The SPR has been approved and will be implemented in WF3 M100:
You opened Call 5717812 with PTC Technical Support on 16-May-2007, with the following description: "Feature reordering in the model tree is unpredictable when the Model has a Footer in it."
Under further investigation, I had opened the Software Performance Report (1370933) so that our Development team could investigate this issue further. Our Development team has now resolved this issue, and resolution details can be seen at https://www.ptc.com/appserver/cs/view/spr.jsp?n=1370933.