Windows 2000 is well past its support date, so it's not really surprising that manufacturers no longer support it. TBH, I find it difficult to believe that FujiFilm haven't released an updated version of your software to work with XP, Vista, or 7. What exactly is it?
If you really are stuck with 2000 then I think that you need to get hold of an older card that supports the OS. But your best bet is to try to find an updated version of your software.