I'm assuming you have the 3G iPod, if not then ignore this. A friend and I worked out a couple theories on this. One is that the iPod won't tell itself to go to sleep when it's connected to the dock. You can even test this by trying to make it go to sleep yourself. So what happens is the battery is constantly being used while on the Dock. Once the computer is asleep, the iPod will no longer be recieving power, and so it will just keep eating away at the battery life. Which as I've found several times means that I wake up with a dead iPod. I agree it's silly, but it appears that if you've got the iPod on the Dock, you should take it off once it's done charging, or at least once the computer is off.