Course Categories only showing Parent Categories

When looking at the Course Category page it is only showing a small subset of the categories. I've found it's only showing the Parent Categories in the list and not showing any of the child categories. This is also affecting the display on the front-end. I have tried adjusting the permalink structure and it's still not showing the children categories. However, if I go to create a new category and select the Parent Dropdown I then see all the categories (Parent and Children). Also the Category list number shows the correct number as well.

Can this be duplicated or is there another step that I need to take? I am running the 1.2.4.3 update and to be honest have had problems with Course Categories following the 1.2.3.4 update. If I roll back to the 1.2.3.3 update then I get the Course Categories to display correctly and also can add extra fields to the Course Categories. All this seems to have problems after updating.

I will include some screenshots in the comments.