Custom Scale Constraint = Upside Down Output

All,

I've been trying to figure out a problem for a week or two now and was hoping some of you might be able to help me out. 

Question: When processing a photo set using a custom scale constraint, how does one influence the Z axis on the output of the model. I am running models no problem through Bentley, but have been unable to figure out how to get any of the outputs to "flip" right side up instead of constantly upside down. I attempted to use some "fake" gcp's as the old Bentley documentation suggested however my scale constraint produces inaccurate results. 

It happens with every output, doesn't matter if it's a point cloud or a mesh.. and I can't understand what we are not doing correctly. I know the SRS is changed when creating a custom scale constraint, but the axis flipping upside down has now become a part of my every day life.

Any tips/tricks welcome!