Melissa,
You have to do a lot of searching on the forums, but this appears to be an issue moodle does not want to shine a light on and doesn't believe to be a bug or incorrect functionality of the restore process. Everything is working 'as it should be' according to them.
Their stance appears to be, and I am paraphrasing since I can't find the post where I read this, that categories should be touched after every restore to ensure that they are setup and configured properly. Makes absolutely no sense to me, since we take the time to configure and setup courses for repeatability during restoring, why would gradebook categories not also be included?
I also have the same issue where categories are not created/kept after the backup/restore process and it's quite frustrating having to recreate the categories from scratch, adjust the numbers to implement the desired grade calculations and repeat as necessary for each separate instance of the course.
There are a number of 'workarounds' in such that they all involve using one course. Which only masks the issue because you're not performing the backup and restore process, so the issue never technically happens.