I had uploaded a bunch of product images and went in and checked off about 20. I processed those, but now when I go back to finish the rest they are not there!
When you use the Process button on the Process Images page it will process all the images listed whether the box to the left is checked or not.
The check boxes are there for DELETING images. You check the images you want remove, and when you hit the DELETE button, only the checked items are deleted.