FWIW, I've seen flash problems frequently in the past where flash adverts video, etc., would overlap part of the web pages I was viewing, where all I needed to do to solve it was change the User Agent to XP running IE versus Linux running Firefox.
IOW, it appears that the way the sites are looking at the User Agent string can impact the way the pages are displayed. I just use Prefbar
for that purpose, since it gives me a drop down list of User Agents I can choose from.
You can also customize the UA strings. But, it's not obvious how to do that part (you have to use the customize menus and click on the User Agent listing in the available menu options and a screen will come up that lets you add more UAs). Using the Firefox customize features, you can drag and drop the Prefbar toolbar someplace else, too. Again, that kind of thing is not very obvious. But, I've got my Firefox setup so that the Prefbar options are to the right of the main toolbar choices (File, Edit, etc.).
You can find other add-ons that let you change the User Agent string returned to web sites, too. You might be surprised at some of the problems you can "fix", just by telling sites you're using a different operating system instead of Linux.
So, I wouldn't rule out that the way sites and flash based players are looking at the User Agent string to be the cause of these types of issues (as I've seen multiple cases where just changing the UA to something else solved overlap problems with flash video on web sites).