Hmm - I have no experience with the Super CCD colour system, odd that RT won't read it correctly though.
Curiousity of course makes me ask if you could email one of your RAF files?
sledger [at] gmail.com
Meantime, Fuji have a RAW decoder for Finepix cams Super CDD
It's free and can be downloaded here
(perhaps this was bundled with your Camera?)
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