> They have added scanlines to the visual pinmame screen.
>
> trouble is that I have it running on my cabinet which only supports 640x480 and
> already has built in scanlines. The vpinmame screen overlaps some of the
> gameboard.
>
> Is there any way to changing the settings on vpinmame?
>
It is not scanlines. A DMD display got space between the dots both vertical and horizontal. You can remove the space between the dots by doing "Controller.AntiAlias=False" before "Controller.Run" (I know that .AntiAlias is a weird name and we will change it in the future)

There is no option to only remove the horizontal space so your dmd will probably look strange if your monitor got scanlines.