When you enter a glossary entries through either the Biblical terms tool or the Biblical terms renderings window, Paratext links those entries to the Biblical term and can determine how to sort the glossary entries. (It uses the sort order in the project settings for this.) If you had manually made glossary entries prior to using the Biblical terms tool, those entries are not linked to any Biblical term for your project and Paratext does not know how to sort them. It is the Biblical terms tool that enables the automatic sorting. You will need to find each glossary term that you entered manually in the Biblical terms tool and establish the link. You can read about this under “How do I associate an existing glossary entry with a Biblical Term” in Paratext Help.
The following video also describes this procedure in more detail: