When I use the PTUI rotate option under the "Crop" or "Mask" tab PTGUI gets completely confused.
To stitch the raw images with PTGui they all have to be in the same orientation. I was able to rotate the individual raw images first in my camera's native raw editor (Viewer 3 for Olympus in my case). All I did was rotate the thumbnail in Viewer, no need to save or anything. Somehow this was enough to correct the orientation before loading into PTGui. Trying the same with any other raw setting had no effect. For example, if I corrected the white balance in the raw images, without exporting, the changes to raw are written to a sidecar file, which PTGui does not read. I'm guessing orientation is somehow written back to the raw file which PTGui can read?
Hope that helps?