Your problem probably possibly can be solved this way. I've also had those clicks while recording through SPDIF. The solution was to set my recording device clock to SPDIF, instead of internal, ADAT, or whatever.
The noises I've been complaining aren't just clicks. The whole sound gets messy, specially the low end, which gets completely noisy, but only when I the guitar through any of the inputs. If I connect my guitar straight to my recording device, running through SPDIF, it sounds ok.
A couple years ago, my Kemper started with digital clips and pops all around, but it only happened while I was plugin the guitar in any of the inputs. While reamping through SPDIF, those clicks had gone. I took the profiler to the only Kemper dealer in Brazil, and they replaced (at least they said they did) the input soundboard. It costed me around U$ 1k at the time. A couple of days ago the problem returned. I don't know if it is really a hardware problem, or maybe it has something to do with the moist weather where I live (South Brazil).
