If I understand your request correctly you want the footnotes always to appear 
bottom of the page? This is what usually should happen, if you do not
use \raggedbottom or similar (irrc).

Try to use the footmisc package. It is probably in your latex-installation, 
if not install it from ctan. 

Write something like this is Documents->Settings-->LaTeX Preamble


To learn more about the footmisc (it has a lot of options):

If this don't work we would need a small lyx file demonstrating the problem.

And please do not top post. It makes it less likely for some of us older 
folks to reply ;-).  (and it is much easier to follow a thread in 
mail-archive when inline quoting is used, just try it :))

Ingar Pareliussen

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