There are 2 different syntax approaches to relative urls. In a CMS like mojoPortal it is better to use the syntax that makes it relative to the root of the site, basically if the relative url starts with / that means the root of the site. The other syntax with ../../, each ../ means to find the root go up one level from here. You had a bunch of ../../../ in your previous url and that may have been the correct path to the root relative to the layout.master file, but the problem is it needs to be relative to the url of the page not the layout.master file. So the easiest way is to use the syntax with urls relative to the root of the site because this will work correctly no matter the url of the page. So actually I think your previous url for the flash was incorrect, all those ../../ pointed to a location actually higher than the root of the site. The reason it worked in some browsers is because in general browsers are very forgiving of incorrect markup, some browsers are more forgiving than others for some types of issues. So my guess is some browsers compensate for a ../../ syntax that points higher than the root and they figure out where root is correctly.
The ../../ kind of syntax was more useful when using static html files located in folders on disk but in a CMS I recommend always use urls relative to the root of the site, they are easier to read and they will work no matter what the url of the page is.
Hope it helps,