I do not believe there were huge numbers of slaves, FMC or otherwise listed in the main ranks but there may have been more in the 'Home Guard' than thought. I can also see there could have been deliberate cleaning of records to downsize the numbers who may have been involved. Even though they 'won' in the end, the North wouldn't look so perfect if records show a number of Blacks who were willing to fight and enlisted in the Confederate Army. That would defeat the purpose that many in the north thought was the real cause for the entire mess. Fight to set them free and then find out that some of them fought you to keep you from setting them free. Ego buster for sure.
Another area I've heard something somewhere on but do not know where to start finding any fact on is the multi-racial soldier. If one was half of one and half another, even if the legal term was Negro, if they were trusted and knew how to shoot straight, they could have passed.