New answers tagged panorama
Photoshop tries to detect the correct order and reorder them for you, based on the edges lining up. So to answer the why side, PS is probably confused based on the photographs' content about what order they go in. Several answers suggest using a different stitcher that allows you to specify the correct order manually, likely the best option.
What you are looking for is a software that can make some kind of stitching. It's not really a classical projection as those tend to project a sphere into something else (you generally take pictures using a tripod and just rotate the camera, not moving it). You really don't want cylindrical projections (which are projections from a sphere to a plan) or ...
If you are on Windows platform, try Microsoft Image Composite Editor. It has mode for this kind of stitching and it works quite well.
What you are looking for is Rectilinear projection. It practice, it is usually hard to get right, since it tends to amplify mis-alignments of individual images. See for example this tutorial or this one for an example of stitching flat images together.
Hugin panotools has a mosaic-scan stitching mode (vs the usual rotating-camera mode) that correctly handles the perspective issues from the camera moving. See, for example, a Hugin tutorial, which begins by saying Normal panoramas are stitched from a number of photos taken from the same location such that the nodal point of the lens stays stationary and ...
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