Publishing Problem

I just recently upgraded to CS3 and I love it. I have my folders set up like

deploy/index.html - for my html page
deploy/swf/main.swf - for my swf
deploy/xml/navigation.xml - for my xml

When I test my fla everything works correctly and there are no problems. When I publish everything shows up except for my navigation. I checked the paths and everything is correct because the swf works, since I am able to see everything else.

The only way my navigation shows up is when I put the swf in the same directory as the html page. But when I put it in another folder and change the paths only my navigation wont show up but everything else will.

Has anyone had a problem similiar to this?