Quoted from Gov:some of those types of things on the B/W are unavoidable unfortunately. The transitions they used were random and there is not way to accurately detect what screen is going from what. There are some on JD that are the same way. I tried to black most of those out, that is why there are some blank screens on it between animations on it. Nature of the beast it seems.
Would it be possible to release two roms? One with monochrome transitions and one with black? I personally don't like the missing transitions on Shadow. I wouldn't mind if they were a dark neutral color like Blue....or red to match Shadow's cape. It feels like a bug when it goes black, IMO.