Hi, NH,
I think I figured out a workaround for this. It makes the process semi-manual rather than fully automated but it should work.
1. Set up a Flats sequence for ONE filter only (e.g., Red), using the auto-ADU (e.g. 35,000).
2. Ekos will figure out the exposure necessary to get that ADU with that filter and take the sequence for as many flat frames as you specified. When it does, you'll notice that the Expoure time it chooses now appears in the Exposure box under Capture Settings.
3. Now change the TYPE only to Dark, don't change any other exposure settings. The exposure time will now be the same as for the flats. You may wish to save the flat darks to another folder...
4. Now click the "+" sign to add this newly-created Dark sequence to the list and click the "play" button.
5. You now have flats and flat darks for that one filter (Red in this case). Repeat the same steps for the other filters.
6. Voila!
7. Make sure to label the flat darks and the darks you take for the light frames differently!

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