Could be something to do with the differences between rubbers that are otherwise identical apart for playing characteristics caused by the rubber colour. I've read several reviews before where a player has tested a particular rubber and said that it plays slightly differently in red than it does in black, even when sponge thickness is the same. I could be imagining this, but every time I've seen this sort of review, it's usually stated that the black colour version plays a bit more offensively than the red.
I assume the different dyes used in red and black rubber must have some effect on how the rubber plays...most of us are probably just not playing at a level where we can notice these differences (or don't test an identical rubber in both colours in order to do the comparison).
Just as an aside, I'm not a pen holder but I always play with black on my FH as I remember reading an article somewhere which stated that this is what most of the pros do (maybe for the reason of offensive play highlighted above). For me it would just seem wierd now if I were to switch to red on the FH.