The colors are indeed quite a bit different. Most of them look pretty damn good though.
By missing areas do you mean the deserts in the Middle East? There was almost no settlement in those areas so them being wastelands makes sense.
Yeah and other areas near Almohads etc...England's color is quite strange mate...dark grey...something is wrong here...I have crashes when I back in the main screen also...
EDIT: I will gave it a manually try now...