I would think that Batch should work if you craft the action well and it can save the files into a folder other then your desktop. You need to select the source and output folders and check override save as steps. The output files should be the document name with a serial number suffix. I think the problem your having is you creating new documents and pasting into them. Instead try recording your action this way. Select the first starboard image do an image crop then save as tiff to your desktop. Do not change the document name. Once save use the history palette to revert back in time to just before yor select starboard image 1. Then Select starboard image two, crop and do the same save as tiff to your desktop. Reply yes to replace the file on your desk top. Then use the history palette to revert back to before you select starboard image two now select image three, crop and do the same save as end the action with close no save.
Thanks so much JJMack!!
Hm, we actually can't use the crop tool as it is too inaccurate and our crop has to match perfectly with the selected channel (which captures the exact dimensions and location of the panel). Is there any way to match the crop with channel? Or any way to make the crop tool more precise to line up with the box of the panel?
Yes you use the alpha to crop load Alpha channel panel 1as a selection then do menu Image>crop Save Panel 1 don't change the image name, Then use history to go back before the crop load alpha channel panel2 etc, Record the action I described above,
Thank you so much!