I’ll put the fix into a new beta and post it in this http://www.thinkboxsoftware.com/krakatoa-downloads/beta-builds/ portion of the website. When it becomes the “official” release is based on the alignment of moons and the roll of a twenty sided die.
FumeFX’s Fire renders as Emission in Krakatoa, so when you change the Emission Strength the overall brightness of the fire is affected. In your case, you need to set the Emission Strength equal to the Final Pass Density when saving to PRT files (and increase the "Generate Emission from FumeFX Fire-> Multiplier to compensate. You’ll probably use whatever is there now times (1 / 0.4) since you are changing the Emission Strength from 1 to 0.4). This way the saved lighting won’t be overblown, and the fire won’t be reduced.
We are looking at ways to fix the workflow to make it less crazy, but this is what you need to do right now. 