Wasn't the title and first example already about a Walk synth?
It took me a while to get a handle on what you were reporting here.
In other words, you're saying that in real life the shots were taken as you moved forward and although the synth begins with the correct first photo and moves chronologically through the photos, the reconstructed camera positions move in the opposite direction (backward)?
The first time I read this, I believed you to be reporting the navigation arrows and movement through the synth when manually moving was backwards.
I would point out that with only the clouds and the ever changing surface of the ocean to go on in most of the frames, there's plenty of room for error, but it is surprising that Photosynth also misinterpreted the shots with the shore.
More example synths would probably help the team further diagnose what is going wrong and what they might be able to do about it.