I haven't use linux for a while, when I did, I noticed such problem, although Im not sure if the grey box is part of the problem of compiz fusion.
I don't think this should be blamed on firefox, flash support isn't good from adobe on mac too, on top of that, linux distroes does not provided adequate support if users were to download and install browsers from vendor's websites, they are expected to use the pre-installed browsers. Which is fine to certain degree.
If there is anything mozilla can do, you can submit bug report any time you want, but I do not think firefox can include non-open codes like flash in its release. 3.5 does include ogg codecs tho. Which I hope helps the situation a bit, albeit ogg still needs more improvement.