I ended up just closing InDesign and pressing Package again. That worked so InDesign must just have been tired and just needed rebooting.
Thanks for the answer, though! I will use this next time something messes up.
I had the same issue and tried using some of Peter's tips to no avail - at least not for this instance.
Then when I exported again, I looked at the file name I was putting in the 'Filename' input field and realized I had a '/' in the name. I'm guessing InD doesn't like any strange characters or / and \. As soon as I switched it to a '-' it worked just fine.
Hope that helps!