Problem solved. I don't know if it's down to the PCB running a higher resolution or not (it would seem like a logical leap of faith), but some screens just can't cope with the full draw area of these boards, hence the flickering longer/shorter far left scanline. However, the game doesn't actually use all the space in the generated picture - I noticed when turning the brightness up there was a whole load of active screen with nothing in it, on the right:
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##########....
##########....
##########....
##########....
##########....
|#########....
,#########....
,#########....
,#########....
,#########....
,#########....
,#########....
(# = pixels, . = unused scanline
, = dead areas of far left scanline, | = flickering part of far left scanline)
I also noticed the screen during bootup, moved to the left by about 15-20 pixels. It's a fairly recent invention, but some games now have position adjustment in test mode. Mushi does. Mine was set to '00' (it's hex) which I believe is the default. Greater numbers move the image to the left (up the scanlines), smaller numbers (wrap to FF and down) to the right (down the scanlines).
So, I moved it to the right a bit, end result:
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..##########..
..##########..
..##########..
..##########..
..##########..
,.##########..
,.##########..
,.##########..
,.##########..
,.##########..
,.##########..
,.##########..
(# = pixels, . = empty scanlines, , = probably half dead scanline area, now unused)
So, there you go - some screens can't cope with higher than usual resolution, and if you try to draw too many scanlines, the screen is unable to complete the full picture within the sync interval. I think that's what's happening anyway. I guess that's why they put in the position adjust (cross hatch option in test menu).