Hmmm... interesting
I must admit that I've never done any of these stitching panoramas so I'm not an expert by any means. I hadn't realised that they did them diagonally, I just thought they 'merged-in' somehow.
One thing comes to mind - many lenses show vignetting where the edges of the frame are slightly darker than the centre so if you've merged the very edge of the left hand shot, say, with a more central part of the right hand shot this might be one cause. Have a look at the original files - just crop the overlap bit, temporarily, from each shot, then compare them side by side to see if they have the same density.
Also, have a look at the exif data for each shot to make sure that the camera did indeed give identical exposures
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