This is the same in the original interpreter, but I assume
they just don't update the screen as much as we do.
The problem is that the new scene palette is
generated and set before the new scene is actually drawn. So there is a moment where the old scene is visible with the new palette...
Reorganize all files in sub directories. The file placement isn't as intuitive as it might be for other engines, which is probably the reason why this hasn't been done before.