Yes, I noticed that too. Images taken in portrait, long side up. Images loaded vertical correctly. Previewing was correct side up. But when looking at the stitched image in Photoshop... it were inverted. Sometimes PS caught it and inverted them correctly. I think there is a flag inside the stitched image header indicating to PS to invert it before display.
Don't recall how I fixed it. I don't think the fix was inside PW4.. I think it had to do with the original image orientation being stitched.
I have been taking 3 fisheye using Sigma 8 and Canon 5d. No issue with this combination. Might have only been with my 20d 4 drum type images.
Let me think on it.
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Dave
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