I have had this problem for a quite a while. The problem is that on certain websites the flash content is only shown only a fraction of its window. For example see http://doom3.com
This only occurs with firefox. Mozilla is OK.
the only thing on the console uppon startup is
(firefox-bin:6177): Gdk-WARNING **: gdk_property_get(): length value has wrapped in calculation (did you pass G_MAXLONG?)
Running FC4 x86_64, using 32 bit browsers.