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I tried it with a rectangular image and it was fine.

Yeah that's right, when every option is checked there is no need for an 'All' option. If you un-check any one of the options the 'All' will become available again.

The only other thing I can suggest is to open 2 images in PS, each in its own tab. You can do this from File > Open and select at least 2 images......at that size you may struggle to get more I dunno, if you've enough RAM you may be able to open more.

Have the 'Base' image in the first tab, you can drag the tabs to re-order them if you need to.

Set the second image as active, in other words click its tab.

Select the 'Move Tool'. Now click on the image and drag it ONTO the first tab......wait until it opens......hold down SHIFT and drop it onto the document.

It should align exactly with the 'Base' image and be on its own layer.

What SHIFT does is to 'center' the layer when you drop it.....as the layer is exactly the same size it'll just fit straight in.

This should work without any trouble although whether its practical or not for your situation I dunno.

Regards.

MrTom.