Why is my single test image much brighter than our Stackshot image output?

Question

I'm working on taking stacked photos of small insect specimens for a university. I am using a Canon EOS 6D body camera. We are using a StackShot macro rail to image these specimens. An issue that has come up is that the images taken in Stackshot look different than the images on the Canon EOS Utility software test shot. They are much darker and look as if the flash is not firing on the StackShot photos, but the flash is firing. I'm wondering if this is a mismatch between the flash firing and the shutter going off within StackShot or if there are other troubleshooting methods I should go through. I've changed the batteries of both the camera and the flash, as well as turning everything on and off again. Any help would be greatly appreciated. Some photos of the issue are attached below:

Canon EOS test shot:

StackShot photo:

Answer 1

Not an answer but a few things to check:

Are you moving toward or away? If the flash is being set at the same level, then as you move toward, you get more light reflected. If moving away, less light. It doesn't take a lot of move to make a significant difference.

You can check this as a cause by mounting the flash off camera.

Are you using automatic exposure/automatic flash? Find the right flash level manually, and use that.

The white background may be fooling the light meter. I generally find that viewing macro level objects on white on screen has a lot of glare. Consider using a neutral grey or a black background. (Art stores have an amazing variety of coloured cardboard.

If this is the case, you may have the opposite problem on a dark background: The stacked image is overexposed.

Have you inquired with the makers of the software?