I think the solution is pretty simple. I took a look at your fit file, and it's regular. It's black and wait allright, because it's still bayered.
You just have to debayer it.
If you open a RAW file, no matter what format, and you just save it as fit, it will not get debayered. So naturally the resulting fit file will be b/w.
The color information is still there, though. What I did is simply debayer your fit file, and I obtained a correctly colored image.
EDIT: just a guess: are you using BatchFormatConversion or BatchDebayer? BatchDebayer is the correct tool if your images are already calibrated, because it also converts them to color (debayer). BatchFormatConversion just change the format, but the images will still be bayered, so b/w until you have calibrated your images and then converted them to color later.
BTW, if you could tell us what you're trying to do on the whole, it would help. Those kind of tools are nearly always not needed. There's probably a better way to do what you're trying to do using other tools.