There are actually two problems. The first is that the overlay is about 1/2 degree off, apparently intentionally. The second is that the game will center the rudder as soon as your ship is within one degree of the intended course.
It's easy enough to fix the overlay problem in photoshop. Just edit the alpha channel and perform an arbitrary rotation so that the grid lines up exactly top to bottom. The resolution isn't that good anyway, so you won't lose anything. While you're at it, copy and paste the sub silhouette from the stock game to the center of the grid. You may have to move the entire thing a pixel or two to one side to get everything to line up.
As the boat moves, the heading will drift. You can watch your rudder go 3 degrees to one side or the other, then back again, as corrections are made. The game is pretty good at keeping you within one degree of true course, but you can tell on a long leg that you are off to one side at the end of it. Not much to be done about this except use shorter course legs.
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