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Okay, I've gone back and tried a number of things, mostly around making everything full URL's I can find in the file, but to no avail.
I have a feeling it comes down to the javascript file that goes with the .swf file (AC_RunActiveContent.js), because when I changed the location of that script, the pages where the header image isn't showing up had a pop-up box appear saying it needs AC_RunActiveContent.js to run.
When the page can find the script, it just comes up with a white space where the .swf should be running.
I'm still yet to figure out why this is working on the index page, but none of the mod pages. I have only been editing theme.html - if there are other files I should be editing please let me know.
I'm running out of ideas on what I'm doing wrong.