Ryan,
I can't imagine there is anything in the dye itself that would harm them. Perhaps the browns were in the wrong place at the wrong time, and when you moved the diffusers you stirred up hydrogen sulfide or something? From my experience having brooks and browns in my pond, the browns hung out in deeper water near the bottom while the brooks cruised the breakline of the pond.
The fact that only the browns are effected makes me think it's a pathogen thing that the browns have not been exposed to (you said they came from a different hatchery) but the brooks have developed an immunity to. The brooks may have been carriers. Like I said a lot of brook trout will test IPN positive and can even be sold in some areas, but never show any symptoms or problems. I'm not saying it's IPN as it could be another pathogen.
Again what pathogens are the two species tested for from both hatcheries? There should be some required testing.
Don't be surprised if this ends abruptly with no clues.
