Herbert gave you a perfect solution; I'll try and explain a bit what's going wrong. Let me begin by saying that it's easy to reproduce the odd output with amsmath (see also the comments to the question). In amsmath.sty, there are the lines
%%\@tempa\widetilde
%%\@tempa\widehat
and it's indeed good that they're commented out. \@tempa is a command that gives accents a special treatment for better accent positioning, especially for double accents. (Compare Herbert's comment to his answer.) This treatment is given to all the "small" accents, including \check.
Now the following code gives the same odd output as the OP's code.
\documentclass[11 pt]{article}
\usepackage{amsmath}
\makeatletter
\@tempa\widehat
\makeatother
\begin{document}
\[ \widehat{\check{x} g_1} \]
\end{document}
This might explain why \@tempa\widehat is commented out in amsmath.sty.
Now MnSymbol loads amsmath and then calls
\DeclareMathAccent{\widehat}{\mathord}{largesymbols}{’302}
which in turn calls \set@mathaccent. But this is the modified \set@mathaccent from amsmath, so thing again go wrong. A possible fix is to give \widehat a LaTeX type definition back again, but for this you have to know the accent number "3C2:
\documentclass[11 pt]{article}
\usepackage{MnSymbol}
\show\widehat
\def\widehat{\mathaccent"3C2\relax}
\begin{document}
\[ \widehat{\check{x} g_1} \]
\end{document}
Summarizing: To me it looks like a bug in MnSymbol.
amsmathI get a fine output. – Alan Munn Jan 28 '11 at 22:32