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I tried doing a test photosynth in my living room, and by the time I was about 3/4 of the way around, it was trying to overlap with where I started. This happened starting in 2 different spots.
It sounds like you're talking about shooting a mobile panorama with the mobile app.
My first question for you is whether you are pivoting the device on the camera lens (like you should for any panorama app) or instead holding the device out in front of you and swinging it around you (a common beginners' mistake).
Here are a few videos that show how to shoot a panorama: http://bit.ly/howtopano
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?