From the code posted above, I was not able to reproduce the problem. The Flash displayed just fine. To get the Flash to display the same in IE and FF, you need to add the window mode to both the <object> and the <embed>
Code:
<param name="wmode" value="transparent"/>
and
Code:
wmode="transparent"
to the <embed>
Looking at the attached screen shot of the page, I can see part seems to be cut off but I also noticed the scroll bar at the bottom of the page. Apparently part of the page is sticking way out to the right of the rest of the content. I would suggest that you work with just a section of the page to fix first the Flash and then the width issue.
Start with a blank page and just put in your wrapper the navigation and an empty <div> the size of the Flash, but without the Flash content. Give it a background color so you can see what it's doing. Get that section working before adding any other content.
For more help, post a link to the page, it seems that the code posted above must have the bottom cut off, because there are several <div> that are not closed.
Best wishes,
EfV