Well, the thing I'll do it's create an ACTION and then use the FILE/AUTOMATE/BATCH.
The thing it's, Wich ACTION SHOULD I CREATE?
Let's say your scans are right in the top of the scaner's glass but somehow in the middle, well, do a new ACTION and begin recording, run the FILE/AUTOMATE/FIT IMAGE...
Then adjust the size of the image to square proportions, this is same value for Widht and Height, easy.
OK, now you have done that, don't use crop, use CANVAS SIZE and make a size on the values you think that fit properly.
Choose save or Save as and stop the recording of the ACTION.
Now use BATCH on that, and MAYBE will help