Hello, just a thought.
I have an Epson Perfection 3200 Photo and scan negatives as well, using XSane.
With the Epson it is possible to scan a whole film strip and then use a crop command to save an individual frame. The parameters (startx, starty, endx, endy) for the next frame stay the same, except for the height (if the scan is vertical). Add also the empty space between the negatives.
You’ll have to figure out once the exact height values, then you can make a script that does the work for you.