My steady Dual Gauss Cannon Conquest officer tried to get flak cannons into range so often that I completely removed PD from the ship.
Are you sure that's what was going on? The AI makes a distinction between PD and non-PD and a steady officer generally speaking shouldn't do that (unless, perhaps, ordered to Eliminate a target), and I'm not seeing any hints of that behavior with such a loadout. If you've got a case where I can see this behavior in a vanilla simulator setup, I'd love to take a look!
Only mod I have is Detailed Combat Results, are you able to accept a file with saved results from that, or is a version without it better?
I just tested it with two steady officers. Without the flak cannon, the minimum range is 1750 from ATU and the skill, and on autopilot it would happily stay around 1900-2000 units away from Onslaughts/Paragons.
With the flak cannon, even when I changed my fleet doctrine from Aggressive (3) to 2, the Conquest would still try to close to ~1250 range of the Onslaughts or Paragon. This was with a flak cannon in its own weapon group (#7).
Testing the flak cannon in weapon group 4, this did not happen in one run, but happened in subsequent runs. It also happens if I put the flak cannon on the side opposite to the broadside.