inconsistent results

[emaxwell]

I am processing several agricultural fields, 3000+ images. I processed the lower section as one project and got good results. You can see form the picture the imagery overlays the clients SHP file data.
The upper portion when processed as one piece produced bad ghosting (double images) in certain areas so I processed it by individual fields. The fields looked good when viewed individually but when overlaid with each other and with the shapefile data there is obvious scale and rotation issues.
All data sets were processed with GPS camera information so the should have been accurate.
This is not the first time I have processed a project more than once and got different results

[bigben]

Have you also defined GCPs? AFAIK the GPS position from the camera is just used for an initial camera placement and gets optimised during the alignment phase.

[JMR]

GPS on board of the cameras are usually crapy, and have refresh rates that sometimes do not match UAV frame interval. Can you export camera centers just after loading photos and overlay them onto your shp before alignment?. That could help to understand what happened.
Also, if that was not the reason for the so called inconsistency, could you show us your settings in the GCP pane?