I noticed the units for the aerial images layer is esriMeters. Is you landbase in feet?
Hi Andrew. Thanks for the reply. Sorry I forgot that this thread still existed out here.
I was able to fix this problem by adding a simple do-nothing layer at the top of the <Layers> tag in our Page.config file. I temporarily forgot that the topmost layer in the list sets the projection for every layer in the map control. When I made that change to the layer order, it automatically switched us back to our Alliant custom projection again, and the scale tool worked correctly.