I'm trying to understand why when I use an old scanned photograph that I want to crop, Aperture rotates the pic sideways. How do I stop this so I can crop the photo?
Actually, Aperture is not rotating the image on its own. It is showing you, how you rotated the image, when you straigtened it, so that you can better fit your cropping rectangle and take the "straighten" into account. It is a feature and not a bug. I am always straightening the horizon firtst and crop later. This way, I will see, if the straightening will cut off important parts of the image - the feet or head of a person in the image, e.g.
Yes, actually I have used that STRAIGHTEN TOOL before cropping...should I do the crop first and THEN straighten? Is that the key?
Try to crop the apparently rotated image. It will work, and perhaps you may even like it. This way, you can see which part of the image are lost by the straightening.