The picture you sent shows the Notecaddy in an idle state after processing all the hands in your Database. IF you reset notes (File - Reset notes) and have a large enough database you will clearly notice the bar filling up while it processes hands and writes notes.
As far as the differences you are noticing on the sample on same stats. Make sure both stats work exactly the same. Most of those differences come from slightly differrent notes. As you pointed and without more info, the case for that specific stat might be triggered by the size bet percentage options that NC has. This will divide all the sucesses in different buckets for bet size. Something very common as well is that the HM3 stats might account for more positions than the NC stat that might be design for specific positions only.
If you find these differences please open a support ticket and attach to that ticket all the information necessary to replicate the issue you are facing: A sample of HHs, the specific name of the definitions used (both HM3 and NC), a screenshot clearly showing the issue, name of the poker room you are playing on.
How to open a support ticket: https://www.pokertracker.com/guides/PT4 ... bug-report
With this information it will be easier for us to pin point if this is an issue that can be solved or a bug that needs fixing.
Let me know more.