This I can answer for you.
Scanlines are always across the long length of the monitor. This means that on a horizontally mounted monitor, they'll be horizontal. On a vertical monitor, they'll be vertical.
As such, the scanlines will obviously not be the same between the two types of games and should follow the game's orientation in general.
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Try checking the MAME manual at http://docs.mamedev.org
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Re: "correct" scanlines
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Here's an example of the rotate png scanlines...
