I have the same issue when I've corrected a photo's orientation with Photoshop. I'm guessing that the program used to upload the photos here at ATP must detect the original camera settings and adjusts the photo orientation when it believes a photo may be sideways. However, when the photo has already been corrected with a photo editor, the ATP system still gives it an, unneeded, 90-degree turn and the photo ends up sideways again (but in the opposite direction of the original image.) This is conjecture on my part but it fits with the problems that I have specifically with photos that I've rotated to correct the orientation.
I've been meaning to ask Dave about this for months to see if we could have the option to disable the auto-rotate when uploading images.
@Dave
Help, pretty please!