I have found that 99% of the time, you will find that you have a setting different. Perhaps one gradebook is set to show percentages and the other one is set to show points. Don't just look at the grade items and categories page, go through all the settings...
In my many years of troubleshooting the gradebook, I have only ever had one that was simply corrupted and I fixed by backing up and restoring the course. The rest of the time, it is a setting. I would go through all settings include the gradebook display settings - I would bet that you will find a difference somewhere.
Subcategories might affect the calculation slightly but the difference between the way it is showing (points vs percentages) is a setting.