chichiflys Hi. I have just discovered the autoflat option and I do have the same issue with my Nikon D5300.
I've seen on the the ZWO ASIAir facebook group that someone else with a Nikon was having the same issue but he reported that he knew people with Canon that were using that function without any problem so I'm guessing there's some form of compatibility issue with the Nikon DSLRs.
Like you, I've tried to change the brightness, I've switched from USB control to shutter release cable and nothing seem to work.
What I'm puzzled about is the fact that when I start the sequence, the shutter is no triggered, so basically the ASIair just count down to estimate the exposure but no light can come in. It looks like the camera doesn receive the shutter release command when launching the autoflat sequence.