There could be traces of programs left on the harddrive, orphaned folders, etc. Unless the DFU mode does a complete wipe, format, and restore on the phone, then there is a chance Genius or Apple can tell if the phone was jail broken or not.
I find it hard to believe that if you restore a jail broken iPhone in DFU mode that a "Genius" will be able to tell if it was jail broken in the past.