I'm sorry to hear that some comments aren't displaying properly in threaded view. I don't see any recent bugs filed for this and I'm not immediately aware of any configuration issues that might cause this. Since this will likely require direct troubleshooting, I'd recommend submitting a support case in your private Jive Community customer group for assistance. If you're not familiar with the case submission process, please reach out to and coordinate this with your community manager.
Let me know if you had any other questions on this.
At Jive-X 2016.1 plus the 3/4 upgrade, our community experiences a problem with Comments (it has been reported to Jive)
- "Flat" view does not list replies in chronological order, it nests children under parent replies, just like "threaded" but without indentation.