You can view the photos in order of filename (which would be the correct chronological order if you haven't renamed them so that they are out of order when sorted alphabetically) by using the period/fullstop and comma keys of your keyboard. Photosynth tries it's hardest to keep things interesting by starting at the photo with the widest view of the scene and then move around the scene in as logical a manner as possible (spatially). Obviously, it's only a computer program, so its choices may seem a little odd to we humans. :)
You're really talking about a completely different topic, but I feel your frustration as well. Once you've learned a bit more about how Photosynth pieces things together it becomes easier to give it photos that it can match. The Photosynth team has said they're working on tools to help correct our future synths, though.