That's the very same problem I'm having too. I'm using the Windows Phone version on my Samsung Omnia W (with gyroscope). It seems that after about 270 degree of rotation photosynth assume that a complete 360 degree was done trying to overlap the begin with the end of the panorama, resulting in a very ugly to see and completely inaccurate result!
I've tried many times, pivoting around the lens (with the maximum precision that a device in hand allows...) but the result is ever the same. I've tried to move only horizontally or going in zigzag up and down or other strategies, no improvements.
I've tried in locations where the panorama is much detailed so that we can exclude that it overlapped two similar view like sea end and start. From my programmer perspective it's like the app read the gyroscope in a wrong way. It's a real pity because the app is wonderful but 360 degree panorama is a must... What can we do?