Here is the text from a follow up email that Jens Enqvist at Cycore Systems sent me which solves the issue I was having. Of course, the problem was, to a large degree, user error. I wanted to post this message to make sure this thread had some closure for those who may encouter the same problem in the future:
Hi Eric,
I am sure I have found the problem now.
The composition was set to Front camera instead of Active camera. This means that you get a different view in the composition window compared to what you render out.
Unfortunately this is not the only problem. After Effects “orthographic” cameras (Front, Top, Left, etc.) use a matrix which Particle World can not interpret correctly. It is a known bug (we are not the only developers having trouble with this!) but we are looking into solving this. Until then, avoid using the built in camera views I mentioned. This includes for example the 4 view option. It won’t cause any problem as long as you do not try to set up an animation using those views. To set up a particle animation you really must use a composition camera (one that you created) and make sure that your composition is set to Active camera.
I was just about to claim that this is mentioned in the manual when I found out it appears to be missing there. We will naturally add an entry regarding this.