Seagrass stitching issues

I am trying to use the software to stitch seagrass beds. The images are georeferenced, very high overlap, I have measuring tapes and marker panels down. The software refuses to calibrate any of the images for a point cloud or ortho. For some reason it cannot match the images. I am uncertain what else to do, I can very clearly see matching points in each image and I can manually stitch the images into an ortho using PTGUI and then georeference and scale in QGIS, but it takes forever to complete. I would love if Pix4d could do it for me. 

Any help would be great!