To me, it looks like the first screenshot uses MS .NET, while the second one
uses Mono (thought I don't understand why it'd run Mono by default when
simply launching a file from the explorer). You could make sure and find out
which framework is used with a function like:

public static bool IsMono()
{
        if(Type.GetType("System.MonoType", false) != null)
        {
                return true;
        }
        return false;
}

Native Windows theming will be included in Mono 2.2, due out in December...
So this should fix your problem, I think (unless it only concerns programs
that use Windows.Forms and not GTK#? I don't know, I guess someone else
could clear that up).
-- 
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http://www.nabble.com/Windows-theme-not-applied-tp20758097p20758223.html
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