I'm looking for an answer for this, too... my initial thought was that the "endif;" function would have to occur IN the footer below a second (or whatever number you needed) loop per the multiple loop examples in the documentation...
But that hasn't worked as expected, though I supposed it could have been due to other issues rather than the occurrence of endif in the footer.php file.
Anyone know if closing the loop (using the endif portion there) is a problem? Would it be because the "get_footer" function is inside the loop?
Curious. Of course, I know I could simply redesign the layout for the bit I want to show up there so that my "footer" either ISN'T called/used at all or it comes AFTER the stuff that is currently placed in the footer.
Enquiring minds would love to get illuminated about closing a loop in an INCLUDED file rather than in the actual index, category, page, single or archive template...