Hello aaronfhd,
Just to be sure, are you drawing shapes in Photo view or in Ortho view mode?
Also it is possible that there are some abrupt elevation changes that are smoothened on the mesh?
In principle, you can enable Attach markers to shape vertices option in the Preferences - it will allow to adjust the projections of the shape vertices individually on each photo (you can do that on couple of images), like for regular markers.