I have to Auto-Align Layers twice to make it work correctly
I was working on a problem and discovered this issue. I have a PSD file. I "Save As" the PSD file as a TIFF so they should be the same. Put the TIFF on top of the PSD and chose Auto-Align and set the blending mode of the top Layer to Difference and got this.

I selected the layers AGAIN and chose Auto-Align AGAIN and this time it WORKED as I got this as the Difference. A perfect match.

I tried this on a couple other photos and got the same results. Seems like the Auto-Align doesn't EXACTLY align the first time you use it.
