See related issue here (http://drupal.org/node/994344).
I have created a custom url alias for a custom content type with url alias being "question/[nid]." The content type is being referenced by another node type. I am using the custom breadcrumb module to link from the other node type to the referenced path.
I am developing on a localhost thus making the home path "localhost/drupal." When I test the custom breadcrumb on the node itself it generates a path of "localhost/drupal/drupal/question/[nid]." It seems that pathauto is adding an additional "/drupal" despite it not being a part of the url alias.
I have tried other things with the custom breadcrumb path such as adding the special identifier for pathauto, . It did not fix the issue it produced a different yet still incorrect path of "localhost/drupal/drupalquestion/[nid]"
I am not sure whether it is a custom breadcrumb module issue or a pathauto issue. I am running D6.19 on XAMPP if it means anything.