Hey OP, get any joy on this? I am having the same exact problem. I recorded with this same setup in July and had no problems, but since then I have updated firmware on both my Kemper and my Apollo, and now it's there.
No.. Kinda strange. Sometimes its there sometimes its not. I leave S/R convert OFF at all times because.. Well the kemper is clocking, no need to convert. I really only notice it on the DI's if ever. But it's inconsistent. If I had to guess, I'd say its the kemper.