Weather let me shot last night so I can send you the log file. I'm not sure if you'll got the informations you need...
The last lines concerning focus module are :
[2017-09-01T00:56:33.666 CEST DEBG ][ org.kde.kstars.ekos.capture] - Requesting focusing if HFR > 2.147[2017-09-01T00:56:33.666 CEST DEBG ][ org.kde.kstars.ekos.focus] - Check Focus requested with minimum required HFR 2.147[2017-09-01T00:56:33.666 CEST INFO ][ org.kde.kstars.ekos.focus] - "Capture d'une image..."
[2017-09-01T00:56:43.645 CEST INFO ][ org.kde.kstars.ekos.focus] - "Image capturée."
[2017-09-01T00:56:43.820 CEST DEBG ][ org.kde.kstars.ekos.focus] - Focus newFITS # 1 : Current HFR 1.84068[2017-09-01T00:56:43.820 CEST INFO ][ org.kde.kstars.ekos.focus] - "Capture d'une image..."
[2017-09-01T00:56:53.926 CEST INFO ][ org.kde.kstars.ekos.focus] - "Image capturée."
[2017-09-01T00:56:54.100 CEST DEBG ][ org.kde.kstars.ekos.focus] - Focus newFITS # 2 : Current HFR 1.75086
It took 2 images because I set an averaging of 2 images for the focus. As you can see the focus is under the threshold, so everything should be fine. But, the capture module doesn't receive the information and is still waiting for focus module to terminate.
Well... disabling the "autofocus after filter change" doesn't change anything, still facing the problem.
Next step is to disable "autofocus if hfr is > xx" and enable "autofocus every xx minutes"