This may be a shortcoming of the UI, more than anything else. There's definitely room for improvement here as I often miss updates to threaded conversations even as I'm looking for them.

I think they could make threads work with some simple changes:

* Optionally show thread replies in-line with chat, as they come in, just like regular chat but with some special annotation to indicate they're part of a thread.

* Allow the user to collapse a thread so they no longer see it in-line.

* Auto-close threads after they're idle for more than 1 hour (or some site-policy-configurable timespan).

* Allow the user to navigate between threads using only their keyboard.

As they are now, I think threads are bad for business. They hide useful information away and slow conversation (responses dragged out because they're no longer in your face).