Unless installing the appropriate Flash and Java plugins fix the problem, you'll just have to accept that some sites and/or features still don't work right in Firefox. For instance, when using Firefox I am unable to use the HTML formatting options in Yahoo! Mail...the options are not available. The Mozilla team is always fixing small things like that (on a larger scale, Pogo, Yahoo, Boxerjam, and other online games didn't work with Firefox for quite some time), but it may take a while for the compatibility issues to be worked out. Hopefully the website/program creator/ISP will meet Mozilla half way, making their services compatible with alternative browsers. In the mean time you may have to use IE occasionally to maintain full functionality.

Hope this helps,
John