Maybe my solution will help you.
My C# "application" is a class library/dll used as a CustomAction for WIX. I wanted a TaskDialog instead of MessageBox but I ran into the same exception as you, and manifest files don't work for C# class libraries as far as I know. I had to use a combination of things to get my code to load the right version of comctl32.dll.
I just got it working so my code is a little messy and fatty.
Sources:
- http://truecheaters.com/f51/%5Bc-%5D-taskdialog-9368.html
- http://support.microsoft.com/kb/830033
1) Include the EnableThemingInScope class as-is from the second link above.
2) Include this modified TaskDialog enums/class:
[Flags]
public enum TaskDialogButtons {
    OK = 0x0001,
    Cancel = 0x0008,
    Yes = 0x0002,
    No = 0x0004,
    Retry = 0x0010,
    Close = 0x0020
}
public enum TaskDialogIcon {
    Information = UInt16.MaxValue - 2,
    Warning = UInt16.MaxValue,
    Stop = UInt16.MaxValue - 1,
    Question = 0,
    SecurityWarning = UInt16.MaxValue - 5,
    SecurityError = UInt16.MaxValue - 6,
    SecuritySuccess = UInt16.MaxValue - 7,
    SecurityShield = UInt16.MaxValue - 3,
    SecurityShieldBlue = UInt16.MaxValue - 4,
    SecurityShieldGray = UInt16.MaxValue - 8
}
public enum TaskDialogResult {
    None,
    OK,
    Cancel,
    Yes,
    No,
    Retry,
    Close
}
public class StatusDialog {
    #region API
    [DllImport( "comctl32.dll", CharSet = CharSet.Unicode )]
    public static extern int TaskDialog( IntPtr hWndParent, IntPtr hInstance, string pszWindowTitle, string pszMainInstruction, string pszContent, int dwCommonButtons, IntPtr pszIzon, out int pnButton );
    #endregion
    #region Modal
    public static TaskDialogResult Show( IWin32Window owner, string text ) {
        return Show( owner, text, null, null, TaskDialogButtons.OK );
    }
    public static TaskDialogResult Show( IWin32Window owner, string text, string instruction ) {
        return Show( owner, text, instruction, null, TaskDialogButtons.OK, 0 );
    }
    public static TaskDialogResult Show( IWin32Window owner, string text, string instruction, string caption ) {
        return Show( owner, text, instruction, caption, TaskDialogButtons.OK, 0 );
    }
    public static TaskDialogResult Show( IWin32Window owner, string text, string instruction, string caption, TaskDialogButtons buttons ) {
        return Show( owner, text, instruction, caption, buttons, 0 );
    }
    public static TaskDialogResult Show( IWin32Window owner, string text, string instruction, string caption, TaskDialogButtons buttons, TaskDialogIcon icon ) {
        return ShowInternal( owner.Handle, text, instruction, caption, buttons, icon );
    }
    #endregion
    #region Non-Modal
    public static TaskDialogResult Show( string text ) {
        return Show( text, null, null, TaskDialogButtons.OK );
    }
    public static TaskDialogResult Show( string text, string instruction ) {
        return Show( text, instruction, null, TaskDialogButtons.OK, 0 );
    }
    public static TaskDialogResult Show( string text, string instruction, string caption ) {
        return Show( text, instruction, caption, TaskDialogButtons.OK, 0 );
    }
    public static TaskDialogResult Show( string text, string instruction, string caption, TaskDialogButtons buttons ) {
        return Show( text, instruction, caption, buttons, 0 );
    }
    public static TaskDialogResult Show( string text, string instruction, string caption, TaskDialogButtons buttons, TaskDialogIcon icon ) {
        return ShowInternal( IntPtr.Zero, text, instruction, caption, buttons, icon );
    }
    #endregion
    #region Core Implementation
    private static TaskDialogResult ShowInternal( IntPtr owner, string text, string instruction, string caption, TaskDialogButtons buttons, TaskDialogIcon icon ) {
        int p;
        using ( new EnableThemingInScope( true ) ) {
            int resss = TaskDialog( owner, IntPtr.Zero, caption, instruction, text, (int) buttons, new IntPtr( (int) icon ), out p );
            if ( resss != 0 )
                throw new InvalidOperationException( "Something weird has happened." + resss.ToString() );
        }
        switch ( p ) {
            case 1:
                return TaskDialogResult.OK;
            case 2:
                return TaskDialogResult.Cancel;
            case 4:
                return TaskDialogResult.Retry;
            case 6:
                return TaskDialogResult.Yes;
            case 7:
                return TaskDialogResult.No;
            case 8:
                return TaskDialogResult.Close;
            default:
                return TaskDialogResult.None;
        }
    }
    #endregion
}
3. To call it, simply:
try {
    StatusDialog.Show( "About to test this...", "Heading I won't use.", "Dialog Title", TaskDialogButtons.OK );
} catch ( Exception e ) {
    MessageBox.Show( e.ToString(), "Error Found", MessageBoxButtons.OK );
}
4. Result:
