Hello Matt,
PhotoScan maintains equal calibration for photos in the following cases:
- Photos have the same size and equal EXIF focal length values
- Photos have the same size and unspecified EXIF focal length
- Photos are calibrated manually and manual calibration parameters are the same
It seems that you are using uncalibrated photos of different sizes. In this case, you can either crop the photos to the same size, or calibrate them manually using "Camera Calibration..." command from the "Tools" menu.
For best accuracy it is also recommended to normalize the photos geometrically so that fiducial marks have the same pixel coordinates on all the photos. Unfortunately, PhotoScan currently doesn't support automatic fiducial marks detection, so this normalization should be performed in the external software.
With best regards,
Dmitry Semyonov
AgiSoft LLC