When i run swfobject to display FLV's along with regular SWF files, my FLV's don't show. I ended up adding <script type...swfobject.js> before each of my "blog posts" with the FLV's and they all started working again.
I am not sure where your original swfobject.js was placed, but it should be within the <head> tag in your rendered HTML page. By placing it there, the functions can be used/called anywhere/time on the page. You definitely shouldn't need to include the script more than once.