This is a known limitation of the SDK when running HTML views inside the Flex client because of HTML views are displayed in an iFrame layered over the Flex UI.
When a Flex menu or dialog overlaps an HTML view that view is replaced by a generated image of the HTML content. Although that image is not always accurate this is temporary and doesn't affect the plugin. This is done automatically otherwise the iFrame would cut off the Flex component under it. The HTML view is restored correctly as soon as the menu is released or the dialog closed.
The only other alternative is to show an empty view under the menu. You can force this behavior by adding the flag <useHtmlContentImage>false</useHtmlContentImage> in the view definition in plugin.xml.
