Yeah, if you can post a link to the puppet (or send a download link to me specifically) I can take a look and see if I can figure out what's going wrong.
Dan Tull
I sent my puppet file to Dan on the Adobe team and he found that I hadn't made all the eyebrows in my puppet independent (+ sign in layer name in photoshop file) They were independent in the front face view that you see in the video, however they weren't in some side profile faces that are in the original PS puppet file. Going through all of my head layers and marking all of my eyebrows with a "+" sign fixed my problem. Dan noted that it was strange that it was issues in the layers that weren't visible at the time that were causing the problem so perhaps if you're having a similar issue, check your whole puppet, not just what is showing at the time. Thanks so much to Dan and the Adobe Team for this help! Thought I'd share my results here incase someone else has this issue in the future.