The issue you mention with Flowdock, in my experience, only happened for newcomers to the product, they added a button to add an unthreaded comment to a thread

The issue you mention with Flowdock, in my experience, only happened for newcomers to the product, they added a button to add an unthreaded comment to a thread in later versions. I prefer Flowdocks threading model, it's too bad what happened to the product after being bought/sold, but I think it was a superior product.