I'm using MiKTeX 2.9 and have recently installed the Minion Pro fonts for use with pdftex. I followed the instructions available on CTAN to install them.
Everything works as expected, but in place of the Greek letter epsilon I get a box with a cross (see below), and the following warning:

I found the issue was reported here, but I still can't fix it. xelatex works fine, but I'd like to to stick to pdftex so I can use microtype.
\documentclass{article}
\usepackage[T1]{fontenc}
\usepackage{MinionPro}
\begin{document}
Text here. $\epsilon$
\end{document}

UPDATE: a set of instructions for the installation of the up-to-date FontPro scripts with MiKTeX can be found here.

MinionProfont do you have? (You can check withotfinfo.) My (working) version isVersion 2.103;PS 2.000;hotconv 1.0.67;makeotf.lib2.5.29150, which I got from (IIRC)Adobe Reader 10under MacOS X. – Christian Clason Dec 14 '12 at 16:412.103;PS 2.000;hotconv 1.0.67;makeotf.lib2.5.29150(Adobe Reader 10 under Windows 7). – nnunes Dec 16 '12 at 11:20