There seems to be some sort of incompatibility between the newtxmath package and libertine-legacy; the following code fails to compile:
\documentclass{article}
\usepackage[libertine]{newtxmath}
\begin{document}
$a = 1$
\end{document}
when compiled through pdflatex, as it results in latex trying to find a Libertine-nu font which doesn't seem to exist:
kpathsea: Running mktextfm Libertine-nu
/usr/local/texlive/2012/texmf/web2c/mktexnam: Could not map source abbreviation L for Libertine-nu.
/usr/local/texlive/2012/texmf/web2c/mktexnam: Need to update /usr/local/texlive/2012/texmf-dist/fonts/map/fontname/special.map?
mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input Libertine-nu
I installed the latest version of the package from: http://mirrors.ctan.org/install/fonts/libertine-legacy.tds.zip today, and haven't tried this before so don't know if it's a recent breakage or not.
I'd prefer to continue using pdflatex because the microtype package that doesn't seem to work well with lualatex or xelatex yet. Changing the package over to use the libertineotf package and compiling with xelatex does work.

newtx, who is usually very responsive. – egreg Oct 24 '12 at 23:34