Alright, I got some feedback from Focusrite - very responsive and quick, so thumbs up for that .
Actually we have been trying a lot of things.
First of all the current beta driver (available at http://beta.focusrite.com/releases/focusrite_control/) seems to work more reliably - no more blue screens. Yet, the out-of-sync dropouts still appear.
In Standalone mode, i.e., Focusrite 18i20 reset to factory defaults then using the Digial Mixing Preset and no connection to PC, the whole thing works flawlessly. The 18i20 synchronization via S/PDIF works as usual and there are no drop-outs. However, once the USB connection is back online, the out-of-sync issue reappears.
My contact at Focusrite claimed it would be the S/PDIF port of the Kemper. Yet, with a different interface (Tascam US-144 MkII) I don't get such drop-outs. And the S/PDIF port the 18i20 is also working fine. Feeding some audio from the S/PDIF out into the S/PDIF works.
So it stays exciting...