I reset my D800 with the two-button reset and there was no improvement.
I've submitted a bug report.
I'm hoping it's just something stupid on my part!

I'm using the demo version of Helicon Focus.
I'm using a Nikon D800 and Nikon 105mm macro lens.
Camera is set on manual exposure, automatic focus. I've tried both AF-S and AF-C and have the same issues.
I've got good lighting in a studio setting; lots of contrast.
When I DISconnect the USB cable to ...