Could you expand a bit more? Is it any particular visemes? If you record the lipsync, are the visemes in the recorded track jumping around? If using audio, what quality is the audio? (Any background music?) Do other puppets exhibit the same behavior?
Common problems are poor audio quality (so the audio analysis plays up), or if the web cam is on and its the Smile and Surprised faces, maybe insufficient light for the web cam to pick up your facial expressions correctly.