I tried to troubleshoot this issue by running the DVD directly to the projector (using S-Video) as opposed to through the iScan Pro. This allowed me to flip back and forth, to compare.
(1) There was no noticeable difference between the direct feed, and the iScan Pro feed - with respect to timing, that is. The IScan output was much better as far as resolution.
(2) I determined that maybe I was being too discerning when I watched the film for the first time last night. Shrek's voice and the donkey's voice are acceptable. It is only when the princess speaks where I think it is wrong.
(3) So I think it is just the limitations of using animation. I think I recall having a similar comment when I watched ToyStory 2. It was right when I got my home theater, and I was very focused on every little thing. Then all other motion picture DVDs never had an issue.