Creating file paths with taxonomy tokens - no sub-tokens

In D6 I used "pathauto", "filefield_paths" and "token" to create a document library folder structure (Windows) based on taxonomy terms. E.g. if the taxonomy vocab was "Document Library" with terms like:
-PATIENT SERVICES
--Forms for Patient Care
---Orthopaedics
and I uploaded a document called "Knee Template.pdf" via a filefield field in a node linked to the term "Orthopedics", then inside the "files" folder I'd get:
"\Document Library\PATIENT SERVICES\Forms for Patient Care\Orthopaedics\Knee Template.pdf".

I used either [termpath-raw] or [catpath-raw].

I've upgraded to D7. [termpath] and [catpath] have gone. When I edit the "document" field I get "File (field) Path Settings" and under that "Replacement Patterns". Expanding the "node" token list I see the taxonomy vocab "Document Library" with the token "[node:taxonomy_vocabulary_2]" but there are no sub-tokens of this to allow me to create a path based on the parents and roots of the taxonomy term.

If I go to "url aliases" (admin/config/search/path/patterns) then under "Replacement Patterns" there are all the taxonomy tokens I could wish for under "Taxonomy Term Paths".

I tried the Entity API and tokens which work but create a messy duplicated token list.

I'm missing something here but I don't know what. This issue is seriously delaying my move to a production site using D7. Any advice greatly appreciated.

D7.12
File (Field) Paths 7.x-1.0-beta3
Pathauto 7.x-1.0
Token 7.x-1.0

Phil