Not pedal/pot related (my assumption but it's auto swell) though a mucky gtr pot would suffer badly on this patch!
I don't think it's the S/PDIF - the headphone out carries the same noise. I tried various sample rates with no difference. Also disconnected S/PDIF and used headphone - noise still audible.
With a Les Paul, It's passable but, with a Strat, it become a bit lively.
The tiniest of touches or scrapes are magnified in the delay 'soup' It's more noticeable on the treble strings
Chords played with lower note included tend to work as intended but single notes on the upper strings are horrible (first reflection and flutter)
So, from your post, I'm guessing something has changed (maybe a gate response speed) as you didn't have a problem before. Sorry not to be more helpful.
Worth sending a ticket, I reckon
The only reason I brought it up is because I was tracking with it on a song (pre-update) and it was fine but when I came to track after the update I was getting that weird swell pop sound.
I'll raise it with Kemper.