Steve, normally when doing master dark frame optimization, both a master bias and master dark are specified. This would typically be done both for flat and light calibrations. You did not specify a master bias, and I am not sure what the dark frame optimize option does with no bias specified, maybe nothing at all?
My own preference for long darks that are both time and temperature matched, is to disable master dark optimize, not specify a master bias, and just have the master dark simply subtracted from the flat or light frame. My detector on 2400s darks has a lot of annoying warm pixels and trying to scale them the same way as normal pixels as well as trying to measure a useful noise metric just does not make sense IMO.
Thanks,
Mike