Try adding \flushbottom to the preamble. If I understand things correctly, LaTeX takes a bit of license with the vertical length of the text body on a page in most document classes (including article, which you're using), but not in books or two-sided documents. The \flushbottom command will (I think) mimic the behavior of a book class and make the bottom edges of the text area on all pages (other than short pages) pretty even.
If it works but you don't like side effects (added vertical space on other pages), you can try insert \flushbottom in ERT a bit before the offending equation and \raggedbottom in ERT a bit after. /Paul
