I'm still trying to run this down. What I've been able to observe is that for one of my Gmail accounts, this never happens, but for my primary account it does.
The issue seems to arise from the fact that some tr.zA.zE.zB.inboxsdk__thread_row rows do not get assigned a data-inboxsdk-threadid attribute.
I've changed the settings in my primary Gmail account to match the account that works, but haven't been able to narrow it down to a simple, "Turn off X settting and it goes away" scenario.
Still very confused, but doing my best to find the underlying problem here and offer a resolution. Any directional guidance is appreciated.