I have an idea what might be causing this. At present we support chroma keying only for paletted textures. If a game uses chroma keying with 565 textures then it wont work.
It is fairly awkward to do. one way is to convert the 565 texture to a 1555 texture and set the alpha bit to zero just for the chroma key color, but that loses colour information.
A better way is to use multitexturing, with one OpenGL texture doing the colour and the other doing the alpha. That's fairly difficult but the trick is already being used for AP88 textures so it may not be too difficult. I might give it a try.
I think Extreme Assault suffers with the same problem, because there are some trees that have all their branches surrounded by black.