Are you 100% sure you're using the latest version of Prodigy? Based on what you describe, including your other thread, it really sounds like you ended up with the old image_manual UI that didn't yet support resizing boxes and didn't yet generate x/y/width/height.
Maybe double-check that you're definitely on the right version and that you haven't set "image_manual_legacy": true somewhere in your prodigy.json?