I have the same problem.
When I save an edited file when the file has flash embedded in the html, the saved file no longer loads the flash movie. After some playing around with the resulting html file, I have found that the saved file includes a number of new <param> tags, inside the object tag for the flash, which were not in the original file. When I remove these extra <param> tags from the saved file (not using fileman but a text editor), the flash then loads correctly again when viewing over a web site. It appears that fileman is editing the code correctly except when it comes the objects <param> tags.
So, then, it appears that fileman is adding extra <param> tags to the saved file and at least one of these tags is causing the flash movie not to load in the browser. Why is fileman adding the extra <param> tags that were not in the original html file? Perhaps it is a flash compatibility issue of not understanding the default <param> tags that fileman adds but wouldn't it just be easier not to add the extra tags when they weren't called for to begin with?
How can I turn that off - the adding of the extra, uneeded, <param> tags?