I had a similar issue with crackling only through the second aggregated device while recording in Studio One and mayyyybe seem to have found a fix? I am using a Macbook pro with two Presonus Quantum 2626 devices aggregated - connected both with thunderbolt cables into two plugs in my Macbook and timing with Wordclock. Running Sonoma 14.2.1. When I opened Universal Control, it indicated that it had an update available. After updating, each of my devices had a firmware update recommended which I also updated. After this, I restarted my computer and it seems I had to re-set up my aggregate device in the Audio-Midi setup, etc, but after all of this, the crackling issue has so far been resolved. Hope this helps some others!