Matt, here are the pics I did on zeroing out the scale. You can also see the sacrificial face on the fence. In the first four pics, the sacrificial face is moved a little bit away from the blade, to make the details about the stop block a bit more clear. Anyway, here's how I do it...
First, I set lock the sliding stop down close to touching the blade, then using the micro adjust screw, I make it just barely touch (or clear) the tips of the saw blade:
The next pic shows the scale slid out a little ways, just for a reference:
Then, I moved the scale back towards the fence just to the point where the zero mark is lined up with the edge of the stop block. I know that point is zero:
Once it's set, you can use that edge of the stop block to reference a specific length all along the scale.
I haven't really used the "inside" scale...the one that's exposed when you extend the fence. When I use the stop block with the extended fence, I simply measure the old-fashioned way if I need a specific measurement. If I just need to match an existing cut, I'll use the first piece to set the stop block to the correct distance. (The micro adjust screw comes in real handy for this.) The way I have my sacrificial face set up, I have to loosen one of the screws holding it on to extend the aluminum fence. You can see the floating nut in this pic:
And here's how I usually use the sacrificial fence. When it's set up like this, I don't use the scale. My steel ruler works just fine for setting up the stop block if necessary, but often I'm cutting to a marked line on the piece, so I use the freshly-cut edge of the face as a reference for my mark. If I need two or more pieces to match, I'll cut the first one based on the mark, then set the stop block to match for cutting the other pieces.
The vernier scale on mine is right on zero when the pointy thing is in the notches. (Excuse my highly technical terms there.)
Can you take a picture of the scale on yours? Maybe we can help figure out the problem.
I hope this helps -