When Drupal 6.x dev always returns "page not found"... pages can still be found
A problem with the yet unreleased versions of Drupal 6 is that in some cases Drupal all of a sudden seems to lose all of its paths. In my case it happened when working on a port of an OSInet module from the Drupal 4.7 to Drupal 6 API.
A symptom of the problem can be seen by checking the menu_router
table and finding it to be empty, although it should contain the default site navigation.