Why Some Fields are not Available to Map Using Salesforce Data Loader

Check Field Level Security (FLS)

Check the missing fields' Field Level Security by Profile or by Fields as outlined here.  If the field is hidden, it will not be available to the Data Loader for mapping.  FLS will grant a user access and visibility to that field.  An Administrator can modify the Field Accessibility and Permissions for the affected user's profile.

Fields not available in Data Loader for Mapping

• Auto-Number fields and Formula fields are read-only fields that can't be edited or created.
• Any field not added to a page layout will not be available in the Data Loader for mapping.  All the fields must be added to any of the page layouts for mapping. 
• Custom objects or custom fields may not be available for mapping for various reasons including object deployment status and the Data Loader flag being incorrectly set for "Show all objects" as described in this article.
• For mapping best practices for External ID fields and upserting,  review this article. 
• To better understand Knowledge Article specifics, please see Update Knowledge Base Articles with Data Loader.

Note: If your field names in the Data Loader don't match the fields in your input file, review this Salesforce Help to get field names aligned.