For the running title you need to stop \MakeUpperCase
changing your symbol. One way to this is to define a command for the symbol, which you can use anywhere, and in section titles proceed it by \protect
. A simpler solution is to define the command via \DeclareRobustCommand
:

\documentclass{article}
\usepackage{MnSymbol}
\DeclareRobustCommand{\mysymb}{{\usefont{U}{MnSymbolC}{m}{n}\symbol{"36}}}
\pagestyle{headings}
\begin{document}
\section{Bla-bla \mysymb{} tititi}
\end{document}
Defining the symbol this way allows it to change size with the surrounding text. Note that I have changed \char
to \symbol{...}
as recommended by egreg.