Thanks for posting about your issue.
I am able to see and use the video controls Firefox 3.5.5 Win. I'm not sure if others can recreate your issue, but wanted to let you know that I'm not seeing the problem in the Flex in a Week beta video pop-up windows.
Upgrading to Firefox 3.5.5 is a go. I have this version on my laptop, and I can see the video controls here.
No worries -- I'm glad this could help you out.
One thing that I wanted to share: Oddly enough, after talking to you about this here on the forum, I actually was able to see the "disappearing controls." It had to do with my Zoom levels in Firefox. If you reset those levels back to the default (Command-0 on Mac, in my case), the controls are normal.