Chiming in to say that the replacement mainboard has seemed to fix all my weird USB issues, so it may indeed be a hardware issue.
Took a while as the second replacement mainboard was also damaged upon arrival (bent heatsink/board, yikes!) but support sent out another replacement shortly after (next day IIRC). The third replacement arrived undamaged and worked.
Also, the new one came with the Tempo audio chip (my previous was Realtek). It worked out of the box in Linux (Fedora), but I couldn’t get it to work in Windows until I found and uninstalled conflicting Realtek software, then re-installed the Framework driver bundle.
I’d say overall incredible support, so if anyone from the team is reading this, thanks again and please keep it up!