With org from cvs (Org-mode version 7.7 (release_7.7.326.g32cf8.dirty)) footnotes don't work properly when inserted in non org files. The first footnote appears above the footnote tag, all the others underneath:
text [1] ... more text [2] [1] footnote ___ [2] footnote This does not happen with the stable version henry -- http://literaturlatenight.de