black rule in Photoshop "sandwich"

Here is a problem I have encountered this past couple of months. When I make a Photoshop "sandwich," I am getting a black outline around all or at least a portion of the top photo after I import to Indesign, and then turn the Indesign document into a PDF. (I use this on the cover of a magazine when I want a person's head to lay on top of a portion of our logo, for example.)

In short, here is what I do:

Open photo in Photoshop
Use wand to highlight image (or capture image).
Copy
Open new Photoshop document, making sure it is transparent, and change picas to inches.
Create a size larger than needed for cropping. Hit “OK”
Paste what was saved into window.
Crop down to fit
Save as Photoshop document (PSD)
Save original picture as Photoshop document (PSD)
Then, in InDesign, place main picture. Drop on the logo over the top of the first picture. Then, place element of picture, making sure to line up the "top" and "bottom" pictures.

This system worked fine for months. But, the past couple of months, I have started to get this black line around the top photo. Two months ago, the photo printed fine, without the black rule. However, this month, the press said the black rule was showing up.

Any ideas?