Looks like it errorr relate to Category module. I crosspost this erorr to Pathauto module. Greggles say:

Frankly, though, I will want proof that this is a problem in pathauto and not just a problem with the way that category module works. Category is a total departure from drupal's core style of handling taxonomy so it's up to category to make itself work with pathauto, in my opinion.

I am trying to use [vocab]/[nid] or [cat]/[nid] patterns for node paths (in Pathauto) and they work fine root/vocab/nid when Bulk generate pathauto run is done... yet upon update of the node I get only the /nid.

I notice that this bug not extend on Category or Container nodes. I have [categorypath]/[nid] pattern for category and container nodes, and url looks fine then i update category or container nodes.

Drupal 5.1, Pathauto 5.1-1.1, Category 5.x-1-x-dev