I also had problems with nested boxes using mdframed
inside a beamerposter
document (nested boxes are quite common on posters). I decided to give tcolorbox
a try, and it has no problems with arbitrarily nested boxes (this is example is stolen from the CTAN package example file):
\documentclass{article}
\usepackage{tcolorbox}
\begin{document}
\section{Boxes in boxes}
\begin{tcolorbox}[colback=yellow!10!white,colframe=yellow!50!black,
every box/.style={fonttitle=\bfseries},title=Box]
\begin{tcolorbox}[enhanced,colback=red!10!white,colframe=red!50!black,
colbacktitle=red!85!black,
title=Box inside box,drop fuzzy shadow]
\begin{tcolorbox}[beamer,colframe=blue!50!black,title=Box inside box inside box]
An now for something completely different: Boxes!\par\medskip
\newtcbox{\mybox}{nobeforeafter,tcbox raise base,colframe=green!50!black,colback=green!10!white,arc=0pt}
\mybox{This} \mybox{is} \mybox{another} \mybox{box.}
\end{tcolorbox}
\end{tcolorbox}
\end{tcolorbox}
\end{document}
Have a look at the beautiful documentation with lots of examples. Especially noteworthy are the available skins, e.g. the "enhanced" skin which uses TikZ
internally. With this, you can create box designs you would not have thought are possible in Latex, have a look here.
So while this might not solve your problem, it provides a good alternative for typesetting nested framed boxes in Latex.