The only thing I can think of that could go wrong with autostiching are the following two: Sorry this might sound stupid.
Loading Pictures in wrong Order (happens to me sometimes)
Shots 0 degree, 240 degree, 120 degree instead of
Shot 0 degree 120 degree, 240 degree.
Second problem that could accure.
The white ring around your panos are not exactelly where they should be.
I used x 800 y 1009 radius 714 on my last panos. Check if this might be the problem.
But then again these are just wild guesses.
More infos needed.
Regards Markus
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