I think this is what is happening:
When you upload an image, WPML Media parses the metadata, and instead of just returning the usual metadata to the apply_filters command from which it was called, it also updates the metadata in the database.
EWWW then runs a few milliseconds later, and it checks to see if metadata exists in the database to determine if the image is a new upload, or an existing one being run through the bulk optimizer. If EWWW thinks it is NOT a new image, and you don’t have the “Resize existing images” option checked, then it skips the resize routine.
I’ve got an idea on a fix, going to see if it works.
In the meantime, you can just turn on “resize existing images” and it should work.