I shot a 360x180 pano early in the morning when the sun was still low causing it to cast very long shadows of myself and the tripod across the floor. In order to edit these out of the nadir shot and a front shot, I manually brought them into Photoshop and used content-aware to remove them. I then brought them into AutoPano Giga and ran the detection... it's result was completely warped.

However, when I ran the detection in APG with the images straight off the camera (unedited for the shadows), APG was able to perfectly stitch everything together... this leads me to believe that the metadata was lost between the camera going in and out of Photoshop. I also tried to edit the image properties while in APG because it no longer recognizes that I used a fisheye lens (In this pano I combined 16mm, 50mm, and 200mm) but that would give me an error saying "you cannot mix fisheye lens with standard lens" even though APG could detect the Pano with the mixed focal lengths when the images were straight off the camera.

Another method I tried was to save the perfectly stitched pano as a template in APG, opened up the group with the edited images, detected using the template from the well stitched pano and the result was still warped.

Anyone have any ideas to what is going on here? Screenshots below of edited pictures in Photoshop and APG. Thanks!