Among the many problems I have with Autopano Pro Video, here is another. First, know that my 6 videos are ok, the clap sync is perfect on every video and no sound comes hinder synchronization. Moreover, Autopano Pro Video synchronization is no problem. Yet see the result!
The problem is that you don't have enough overlap between your video frames at current time. You have to choose a "better moment" to stitch. Stitch is made at timeline current time, so try to seek at a moment when rig is not too close of a wall.
Ok I solved the problems of stitching and synchronization, but I still have a big problem with the length of my movies. I still can not generate video over 1'19''! If for example I want a video of 1'20'', the final render will result in 6 secondes of video followed by black ! To this problem, add the regular crachs software !