I don't know if this is related to your problem but a recent update to the geometry package caused some conflicts for beamer.
I had some problems with beamer a few days ago but went to http://www.ctan.org/pub/tex-archive/macros/latex2e/contrib/beamer/base/ downloaded beamerbasecompatibility.sty (note that it was updated just in February, whereas most of the rest of the package is from 2007) and over-wrote the existing beamerbasecompatibility.sty in MikTeX. See http://www.tug.org/pipermail/tex-live/2010-February/024834.html and http://www.tug.org/pipermail/tex-live/2010-February/thread.html#24927 for more details. There's an alternative fix, which is to add some code before \documentclass but I don't think this is possible in LyX (although you could always export to straight latex and then add the code in TeXworks or whatever). This alternative is discussed here http://permalink.gmane.org/gmane.comp.tex.live/24852 As an aside, personally I prefer using ERT to add \begin{frame}, \frametitle{Your title here} and \end{frame} directly, instead of using the lyxframe commands, since it leads to a "purer" latex output, but this is just a matter of taste.
