I've found that Photomerge yields the stitched images upside down when I stitch vertical frames horizontally.
I always shoot vertical images with the right grip (shutter button) up, but that never happened in the past. I guess that the orientation information is not correctly recognized. It seems to be a glitch of the current version. FWIW, I currently use D750 with the latest firmware (ver. 1.13), and I set the automatic rotation function "off" (I wonder if it is the reason?)
The stitching quality doesn't seem to be affected, and I just have to rotate the final image 180 degree in CC. But it is a bit annoying.
Is anybody experiencing the same issue?