Searched forums. Seems like maybe linking SWF within the plugin doesn't quite work correctly yet?? Not working for me in IE9. I thought it was a z-index thing so I tried a bunch of CSS to get it and could not.
Also, I noticed that changing wmode from anything besides Window (eg Transparent), hides the SWF completely for me. It simply disappears. You can right-click and get the typical flash menu.