Let’s test it manually instead of batching. Please open that same image from the same source folder that you ran the batch. The do the extract using EZ Green Screen in Photoshop. Then save the image. Now close the image and open the saved image. Is it cropped?
My gut feeling is that the images were probably cropped during a Lightroom export. Did you export the green screen images in lightroom before batching in EZ green Screen? If so then open the exported images in Photoshop before extracting. Are the images already cropped?
Please respond here in the forum (not to the automated email).