I played around with "Playfair Solved.twbx". If it's very similar to your workbook, the problem may be how the y-axis is defined.
I changed it's custom SQL so it showed negative numbers. Even though there were negative values, the y-axis still started with 0.
I then edited the axis by double clicking on the y-axis numbers. Under the general tab, the range was set to Fixed. After changing this to Automatic, the y-axis started in the negative range and all values were seen.
I suspect there's more to this; but I hope this answers your question is some small way at least.
Thank you for trying to help, Marshall. I really appreciate it. Unfortunately, the problem is still there. I tried your technique of modifying the SQL in the original workbook (great idea!) and updating the y-axis accordingly, but the shading still stopped at the x-axis instead of continuing down to the negative line.
A year has passed and I still haven't found a solution to this. Any new ideas? ;-)