I have the same problem using beta 1.6.6
For a bit more detail, if you create a new RGB matrix flow step it works - you can check the matrix color box and then choose the color picker and then color the pixels how you like.
But, if you copy a matrix flow step, the matrix color box will revert to white, and if you attempt to choose a new color for the matrix color box, it will not work, reverts to white.
So the way to create an animation is to choose a new matrix flow step each time.
But, it would be good to fix the bug, as creating animations, one always wants to start from the previous frame and then only adjust the pixels to change in that frame to the next.
Thanks!
brad