I've put the relevant four pages here: http://hepwww.ph.qmul.ac.uk/~moyse/lyx/problem.ps (184kb).
It shows pages 131-134 of the complete thesis, and you can see how the footnote has moved. If I just load the chapter, then do view->pdflatex, then everything is okay. See this for details:
http://hepwww.ph.qmul.ac.uk/~moyse/lyx/correct.ps (64k)
you can try a \clearpage after the last paragraph of page 131.
Herbert
