The layer name “image Etxract” has no floor in it. Remove the mask and taht layer should always be the origial.
Here is what I’m pretty sure is goign on.
When you are running the second batch, I think you are select “Extract+ Edit” instead of “Edit PSD Files”. The extract+ Edit mode will first extract and then pause to edit which isn’t what you want because the images are already extracted. So by selecting that, it flattens the image first which will then look just like the thumbnail from the “Image Extract layer in your screenshot. Then it will re-extract the flattened image again.
If you have first batch “Extract Auto” and saved as PSD, you will then want to run the “Edit PSD Files” batch. This will only open any PSD images without doing any processing at all. It just opens them for you to edit.
You would want to use the “Extract + Edit” for doing batches of images that have not yet been extracted. This will first extract the original images and pause for you to make edits.
Let me know if this is what is going on….. pretty sure it is based on your screenshot.