I have Dreamweaver CS5, and used the "Insert FLV" function to generate a flash video player. It creates a /Scripts directory with two files, swfobject_modified.js, and expressInstall.swf, and it also creates two .swfs in the directory the .html file is located, FLVPlayer_Progressive.swf, and an .swf named after the skin (e.g. Clear_Skin_1.swf).
When I have Dreamweaver generate the HTML code for all this with a relative path, it works. When I give Dreamweaver an absolute path, it doesn't. You can see an example at www.youngstreetdesign.com/staging/flvtest/test.html.
The top is the relative, the second the absolute. The third is something unrelated.
Dreamweaver says "enter relative or absolute path here" in the entry where you give it the video's path, and the documentation says that absolute paths should work, so, I'm at a loss.
The absolute path should be working. To the html page it makes no difference where the file is as long as it can map the file from it's location. The only problem would be if the javascript is hosted on another domain as there would be security issues that would stop it working.
To a html doc in the root of the website the following paths would be identical:
/scripts/file.fla scripts/file.fla
to a html file that was in a folder 1 level up:
/scripts/file.fla ../scripts/file.fla
I would check all your links again to make sure. Have you tried looking using firebug or chrome's developer tools? They should show any 404s that the page is showing so perhaps it can't reach a certain file.