If resetting the preferences doesn’t work then I need you to verify for certain if those images open. Just take a few images that didn’t work and put them in a folder by themselves so that only images that didn’t work are in that folder. Then try batching the folder. Watch what happen when it runs. Here is what I need to know.
1. Does it open the images?
2. If it does open the images, can you see it crop the images on computer screen?
Knowing these things will help narrow down the issue.