All of my filters have names (luminance, red, green, blue, clear) and flats options are set to the appropriate values (exposure, brightness level, number of flats, etc). Not sure why they show nothing in your image. Those settings aren't what I get when the equipment is connected. Also I don't make any changes to the filter section during each test run. Like I mentioned before, it doesn't work if the sequence order is light-flats-darks and it does work if the sequence order is lights-darks-flats. There is a section in one of the logs where it shows there is no "turn light on" command issued during the flats image captures when the sequence is preceded by lights and in the other log there is a "turn light on" command issued when preceded by darks. Can you verify that is the case?
I'll look at the equipment profile again just to be sure but I'm pretty sure it's set up the way it is supposed to be. I agree the filter flats info is buried pretty deep! If you need me to, I can do another run with each scenario and send those log files.