I'd try recording both the SP/DIF and analogue sources separately, each whilst the other is physically-unplugged, Sonic.
IMHO, it sounds like the onboard software mixer in the interface is combining the inputs and introducing a tiny phase-inducing delay to one of them, hence the manifestation predominantly in the high frequencies, where the wavelengths are short and the phase shift is hugely-more-apparent.
The obvious explanation for the minuscule delay to one of them is that only the KPA's analogue outs undergo both a D/A stage (KPA outs) as well as an A/D one (interface's analogue in). Depending how new the interface is, I'm guessing you're probably looking at anywhere from 0.6 to 1.2ms delay at the A/D stage, and the Kemper's D/A conversion time is probably in the same range too, meaning that the combined delay could be anything from roughly 1 to a little more than 2 ms, plenty-enough to be responsible for the drunk-mosquito effect when the signal's combined with the "non-delayed" SP/DIF one.
If it's not in said onboard mixer per-se, it could be that if there's an I/O-routing matrix stored within the interface, both flavours of Kemper feeds are being assigned to the same output/s, which in turn appear as inputs in your DAW, albeit pre-combined. You "innocently" choose the source for recording, and... viola... a mosquito in need of a strong coffee "inexplicably" appears.