Hi I have never experienced that problem :). I guess it should be easy to fix, however, we probably need a minimal lyx file showing the problem.
Try taking halves out and see how far you can get the text down to. (try removing external material as well, and remember to make a back up copy ;) ) If you do not want to post the resulting file to the public list you can email it to me and I will have a quick look at it :) Ingar Pareliussen