I bought a COAX/SPDIF converter, and my Kemper sounds a million times better using SPDIF into my Apollo Twin instead of TRS/TS. Until proven otherwise, I don't think I'm experiencing a problem. It's just that SPDIF sounds better than analog/digital conversion.
Glad you got it sorted. If there is a significant sound difference between analog and spdif then something is out of the ordinary at least. The Apollo analog inputs can be very transparent.