Rail vehicle y-offsets are incorrectly setup as if "Y-Offset for train sprites (0E / 8E)" has been changed, which is not possible for a baseset. This means the sprites are not aligned properly compared to the original baseset:  
Rail vehicle y-offsets are incorrectly setup as if "Y-Offset for train sprites (0E / 8E)" has been changed, which is not possible for a baseset.
This means the sprites are not aligned properly compared to the original baseset: