I have never heard of this issue before. Flash is supposed to sit on top of the browser and the background should not be configurable. It's like watching a movie, you can't change the video while it's playing back.
I'd suggest trying to see if you can download the flash files to your hard drive direct and then play them with a stand alone flash player. Good luck.
I'm taking college classes online and they use Flash modules for the lessons presentations and such. Problem is, the text color in them is white and the images are faded because (as I've found out) the background is supposed to be blue. So whenever bullet points come up for example, i see the BULLETS but not the TEXT. Their tech support has been unable to help me.. o_O (after spending 2 hours with an Indian tech agent and trying to figure out what he was saying) and it seems like there was a way to specify default Flash background colors or browser window colors or somethin, I just don't remember where it was. I've updated Java and flash, and searched through the settings and turned on and off hardware acceleration in Flash. It works on my other computer, but I need it to work on this one. I don't suppose me having a dual core is the problem? It's caused stupid problems with other things before. Will Microsoft's new Silverlight be able to replace Flash for me, or does it use its own filetype? It seems like it should be somethin simple to fix.