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When I was shopping for a new DSLR, I did some experiments with dark frames that showed an interesting behavior with the 6D and I suspected that it might result in exactly what you are describing. I didn't take it any further as I decided that the 70D was a better overall camera for me.
Essentially I took a 30 second dark frame (LENR off) at each ISO setting for each camera and then looked at the mean and standard deviation of the noise in the RAW files. You can see the same information by looking at the histogram on the camera which moves towards the right and gets wider as the noise goes up, as you'd expect. With the 6D there was a point where the histogram suddenly goes back to the left axis but the width of the histogram (std dev) stays the same, inferring that the camera is doing a pseudo dark subtraction. This is happening prior to the RAW file.
I didn't do any tests with a constant ISO and increasing exposure time but if the same thing occurs, that would fit with what you are seeing. The camera subtracts a pseudo-dark for the light frames but not for the flat frames because they are a shorter exposure.
This may all be common knowledge or it may be a red herring. I don't know. You might want to experiment further.
Steve.
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