I noticed the same thing. Seems to be a one-way sync only. You would have to somehow let Amazon know where you are in the book and your Kindle would have to have WiFi or 3G left on as you read to keep up the sync.
My advice is to just read different books on each device, or get in the habit of noting the location number, if you insist on only reading one book at a time.
I also noticed the dictionary doesn't work on the iPod like it does on the Kindle. One would have to leave the book and go to the dictionary book; it doesn't seem to be embedded in the reading app like it is in the Kindle.
The iPod app seems to be in its fledgling stage compared to what is on the Kindles.