Would just like to add an issue I came across on one particular site but could not replicate on my own site.
I spoke to Tim about this as it was occurring in the quiz module but he informed me it was an issue with the HTML editor and that you had the best knowledge on how it worked.
Here is what was happening. Entries in a quiz question contained href links referencing a file on the server, such as href="draftfile.php/1/2/somefile.swf", however the link would be formatted with the term @@PLUGINFILE@@ when viewing the html source. Very odd. The solution was to edit the question and delete the URL (make it blank - href="") saving the changes, then re-editing the question and adding the URL again. The only way I can see why this is fixing the issue is if a bug caused these links to be saved incorrectly, and if not altered it is never updated.
Sorry I can't be of more help on this issue.