I've made a few simple puppets, so I'm starting to get the hang of it. However, today I made a puppet in Illustrator and the guy's eyes are going in opposite directions when using the webcam for eye gaze. I've double checked all the tags and made sure they are correctly connected to the head. The only thing I did differently with this puppet is that I used a mask over the eyeball, so that the gradient remained perfectly circular.
Make sure your left/right pupil layers aren't bigger than your left/right pupil range layers (usually the same as your eyeball layers). By default, a group named "Left Eyeball" will get the Left Pupil Range tag (same for "Right"). If you want to control the pupil range independently, you can create another layer of any appearance whose (rectangular) size indicates the correct range, tag it Left Pupil Range in the properties panel tags section, and turn the layer off so it doesn't show up. Also untag the other group tagged Left Pupil Range — there can be only one per view.
Another option: share your puppet so we can diagnose it.
I see how that could also have caused the problem. Of course when I went in to the layer to make some adjustments, I noticed that when I copied/pasted the Left Pupil, I had forgotten to relabel it Right Pupil. Man, there are SO MANY details to maintain! How soon until the computer just knows what we MEANT to do??