Drupal 5.19 - Taxonomy, Terms, Paths, and a Menu.
Hello all,
First of all, loving Drupal. While there were some growing pains at first, I'm happy to say that I've come round to the Drupal way of thinking and finally realise the potential this system has to offer. I've managed to build a sturdy and attractive site that is finally coming together. I've been able to tackle all of the problems I've encountered so far, but this one has me stumped. Be warned: this problem involves a depreciated module.
I have a Vocabulary named "Course". Within this vocabulary are three Terms - "Type", "Subject", and "Profession". Each of these contains child Terms. PathAuto gives each new term a URL based on its hierarchy. For example: Adding a term titled "Degree" as a child of "Type" creates the URL "types/degrees". Using PathAuto and Taxonomy Term Menu (the depreciated module), I have built a menu that displays each of these terms in the right hierarchy. A content editor can add a new Term, click "Menu settings", and complete the form to add their term to the menu.
Now, to get to the point:
The most recently added term appears in the menu, but does not have the correct URL.
For example, I can enter "Author" under "Profession". The URL that is displayed in the menu system should be "professions/author". However, I get "taxonomy/term/67".
Note that the Term itself is correct - at the Terms list, the term will be shown with the URL "professions/author". If I move onto another term and make another addition, the "professions/author" URL is fixed in the menu.
While I appreciate that the use of depreciated modules is generally frowned upon, I would be eternally grateful if anybody could point me in the right direction to a possible solution.

Follow-up and solution
All,
No responses, but I thought I'd follow this up since somebody else might encounter the same problem.
Turns out this issue was patched in the Dev version PathAuto but for some reason never carried over to the live version: http://drupal.org/files/issues/pathauto_taxonomy.inc__0.patch .
It kills me that I spent 2 days agonising over a problem that was solved by just deleting 5 characters of code.