Hi Dmitry,
There are several reasons that can cause this result:
1. Check “Ignore parent progress” setting in the Progress column configuration. (If you don’t see it, then it’s irrelevant.) Turning it on may result in what you need.
2. Make sure that the structure does not contain issues that were deleted from JIRA. Structure may still refer to them by their ID (although it won’t show them). To verify, please ask JIRA admin to go to Administration | Structure | Maintenance and a) check that the daily maintenance is turned on including "Optimize structures” step; b) use “Run Maintenance Now” and turn on “Optimize structures” only.
3. Make sure that you have the permissions to see all issues in the structure. Ask a JIRA admin to open the same structure (you can use “Share” button that will help them open the same column configuration), review it and see if there are any issues that have less than 100% under the root.
Please let me know if this helps.
Kind regards,
Igor