The problem with JPEG files is the EXIF 'orientation' tag and the
rotation sensor of your camera.
If you hold your camera in portrait, the camera actually still creates a
landscape orientation image, but it adds a tag to the EXIF data that
says that the image should be rotated 90 degrees. Some applications
support this, while others ignore the tag and will still show the image
in landscape orientation.
If you open such an image in PTGui, it will load the image as a
landscape image but set the initial roll to +/- 90 degrees. This was
done mainly for compatibility with PTStitcher.
If you open the image and re-save in Photoshop, Photoshop will
physically rotate the image and remove the EXIF orientation tag. So you
will end up with a 'real' portrait image.
So if you modify one image, it will actually get a different
orientation. Also this will probably mess up your control points, since
the x and y coordinates become swapped!
The solution would be to open all your JPEG files in Photoshop and
resave them, before loading them into PTGui. You can then safely edit an
image and convert to TIFF.
Since hardly anybody uses PTStitcher anymore, it might be better if I
change this behaviour, but this is a bit tricky since it needs to stay
backwards compatible with older projects.
Joost