Yes that is how it works.
The focuser must be ASCOM.
To activate the Autofocus you need to put 99999 in the focus section.
Here are screen shots of the sections I referred to.
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Hi Martin, if you are using ver.7 latest service pack. The sequencer can be set up to do what you want. Go to the AA help topics and search for Autofocus to learn how to set it up. Then search for sequence that will explain how to incorporate auto focus in a sequence. Here is a very simple sequence ...
I'm just guessing, since you said your balance was so perfect it might be a slight bit of play in the worm. You may want to try keeping your balance slightly heavy to the East.
In the bottom left corner of your flat there are some numbers, B is the background average. For my 16 bit camera I try to get that value between 25,000 and 30,000. In that range my flats correct very well. For a 12 bit camera you will need a lower range. In the AstroArt help topics search for "Flat ...