This is a recurring issue that I am having now with Anime Studio, which I bought less than a year ago. Mainly, I will edit, arrange, or move something in frame zero and in the video it appears "messed up" or unpredictable and wrong. As this is really difficult to say in writing, I posted a video of this issue on youtube. Please Please check it out and see if anyone else experiences this! The first 12 seconds I didn't know it was recording, but then it starts.
Are you sure you haven't any keyframe beyond zero?
Select each layer and check the if there are any keyframe during the animation, it could be the layers or the points were scaled accidentally.
That's all I can think viewing the video, if it's not the problem, could you upload the anme file to take a look?
Yes, you're right, there were stray Keyframes waaaay ahead on the timeline. I have no idea how they came to be there, but I must be at fault. I hope that's my issue every time, because it is easy to isolate!