Steps to reproduce:
1) Create contact subtypes - Individual - Student and Organization - School was used for testing.
2) Create a relationship (a-b) Student of (Student) - Student for (School).
3) Import contacts using any file, the relationship above does not show up as a choice for mapping.
It only seems to depend on the first part (a) being a subtype or not. This was verified on the demo site.
In addition these relationships can't be exported either.