I've had this issue for forever, thought I'd finally ask about it:
When I create a batch macro, there is often one or two images, out of say twenty, that will not SAVE like all the others in the directory. So, out of 20 images, maybe 2 or 3 will halt the batch macro and require user input.
This phenomenon survives rebooting, and it's always the SAME images that are the culprits. They are being routed into a different directory, so they aren't trying to overwrite an identically named file.
Obviously, since it's just a FRACTION of the files, the macro is constructed properly. Since it survives rebooting, the images aren't open in some other program. SO, what is it about specific images that would prevent Photoshop from correctly saving them, when it saves 19 others no problem?
I would look at the images in question and try to figure out what is different about those images. I once had a similar problem and found some of my images were layered tiffs and that caused the problem.