A couple suggestions that i can offer.
1. In your SPDIF setup, one device has to be the master for sync purposes and the other unit has to be setup as a slave unit. If the two units are not in sync, you will get crappy or no SPDIF audio at all. Your KPA is the master, so make sure to setup your Focusrite to be the slave. By default, it's probably setup to be the master for sync purposes. Most audio interfaces switch from internal clock to external clock automatically when it detects a S/PDIF signal. Not sure about your Focusrite. You may have to manually change it somewhere in the control panel for your Scarlett. If it's currently set to "Internal", change it to external sync, so it gets it's sync timing from the Kemper.
2. Once the two units are in sync, it's just a matter of going to the Master output S/PDIF knob of the Kemper and selecting which audio you want to send to your Focusrite. All of the settings should work, Master Stereo, ect. Some are more specific, like the ones mentioned above. Git/Mod or Got/Master Mono puts the unprocessed guitar from the input jack on one of the two S/PDIF channels and the processed sound on the other S/PDIF channel. The Kemper manual describes all the various options for S/PDIF output. None of them will work if the two units aren't in sync first.
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I am having this same issue. (Old bump, I know)
Attempting to use a Kemper powered toaster with a new Focusrite 6i6 and the free version of Pro Tools that comes with it. (Pro Tools First)
Will give this a shot tonight to see if i can get sound.