I read a few of the manuals that he made and I don't know the exact reason why the compass is inverted.
All you have to do to find the target's bearing is to do the 2 observations as he says in there and draw the line between the 2 observation lines in the map, this compares the distance and time the ship has traveled. If the ship is going from left to right on the map, then the first point on the line that tells you the speed that touches the compass circle is the target bearing. If the ship is going the other way then invert the procedure.
When you're using the ruler tool to draw a line, you drop the first end at a chosen point and drag the rest of the line out in whatever direction you need. The inverted compass around the cursor lets you read that as a heading. So, if you're dragging the line to the south, that's a heading of 180. This way you don't have to flip it in your head.
When you extract version 1.3, unless you've messed with the WinZip configuration, it creates three folders. One is labeled Backup, one is Option, and one is SilentHunterIII. If you want the inverted compass ruler, leave the Option folder alone. The line.tga file in the Option folder is the ruler with the 0 at the north position and 180 at the south. If you're dragging that in, you're overwriting the inverted cursor with the standard.