Photoshop CS6 random color shifts

Question

Here's the lowdown on my system/machine:
Photoshop CS6 (version 13.0.4)
Mac platform, OSX (version 10.8.4)
2 x 2.4 GHz Quad-Core Intel Xeon
I'm having  problems with color shifts in a batch of images from a common Photoshop document.
I make 28 images from a single file, think of it like a picture frame where the frame doesn't change but the art depicted in it changes.
Since they come from the same Photoshop document they all have the same profiles and settings, they are all the same size and the frame should never change color—but it does.
Therein lies the problem.
A color shift in the art wouldn't really be noticable since the art is different every time. The frame is the same across all the images and the shift is obvious in the frame.
We use an Applescript to speed up the process; The script turns on a layer, flattens the image, then saves it out as an EPS for placement in InDesign, reverts to the layered version, then turns on the next layer and repeats the operation.
Of the 28 images, 3 of them have a noticable color shift.
It's never the same images that shift, it's just a random assortment that are effected (right now it happens to be 3, the next set of images may have more or it may have less).
Here's a screen shot of the color build in a specific location on sample 1:
Screenshot of the color build in exactly the same location on sample 2:
Here's a screenshot of the effected files in the directory (those highlighted in green are shifted):
Has anyone else seen this?
After some basic file analysis:
The shift occurs when the person working in the file creates a new document and copies the existing components from the master file into the new file.
I'm still confused since it's done on the same machine, with the same color settings/profiles, by the same person. It is still random.
BAD

Answer 1

Okay then. I mean when I use the Eyedropper Tool on the color that I had already put on a picture, the color becomes darker than what is shown when I use the Brush tool.
Like when I put light red as the foreground color, then switch it out for another color, then used the Eyedropper tool to copy the light red color to use it again, the light red color instead becomes a slight darker red when I use the brush or other related tools I use to color in my picture.
Hope this detail is clear enough.