I'm using ACDSee Pro as well, but I've turned off the display of the thumbnail (it annoyed me) and don't the slightest idea how to bring it back.
I think you can delete the first image = thumbnail by selecting and deleting it. If not, you can delete it in any image editor like Corel Draw or Gimp - sorry, I don't know about Photoshop.
If you convert the image to jpg it will be gone.
If you don't need the 16bit (which some call 48bit) option, just scan @ 8bit tiff.
Maybe ACD can delete it with the batch converter -> from 48 bit to 16 bit? I've never tried it...