Are you saying that you previously had rules that threaded, and with the most recent update you did, it is no longer threading? Or is it that you expected with the update that it would start threading them and it is not doing so?
I’m running discourse 093ee1d80c and discourse-chat-integration da91061 (current up-to-date) and my channel with thread rules is correctly threading responses, only for channels set up with thread rules.
Can you show your configuration for a thread rule? In Admin → Plugins → Chat Integrations you should see rules that say
and if you click on the edit pencil you should see
If you have rules that instead say:
then those rules won’t use threads.
You’ll see above the rationale for this being a per-rule, not per-site, configuration.
When you set up a rule from the /discourse command in slack (or whatever command you chose when you set up the integration), you use thread instead of watch or follow, as documented in Chatroom Integration Plugin (discourse-chat-integration)