Undesired behavior when calibrating cameras

Background:
We are trying to evaluate Pix4D to generate Orthomosaics of images taken of the seabed underwater with autonomous underwater vehicles. For each image the position and altitude is embedded and the navigation accuracy of our vehicle is extremely accurate, so the task should be as simple as "overlaying" the images. I have more than 90% overlap in each image and good detailed conditions.

Current situation:
When I try to process a set of images the calibration process completely skews the image positions, puts them at different altitudes, rotations and positions. I do not understand why this is even possible when all needed information regarding positions of the images is already embedded in the images. 
See the two included images for reference.

I hope someone has the expertise to help me with this.

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