I've updated DLLs to the latest version 2013.3.1016.40. When clicking the top-level header item, it disappears. I have to click and hold the mouse then the sub items will be displayed. This dose not happen to the previous version.
The resource dictionary that you are merging is using our old styles - we have changed RadMenuItem's Implicit Style and using the old one is causing the problem. You can take a look at our new Style inside Telerik.Windows.Controls.Navigation.xaml under <RadControls_Installation_Dir>\Themes.Implicit\WPF40\OfficeBlack directory.
Hopefully this helps. Feel free to contact us in case you have any other problems or concerns.
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