Thank you for your post!
In order to better help you with this, you will need to contact our Support team directly and provide the AI file. I have tested the Split layer function with unique values, as you have described and the names of the created layers should reflect these values. Splitting into subgroups should not be necessary.
If you can reach out to us via help.avenza.com and provide the file(s) we can take a better look and provide you with a solution!