pathauto issue

Not sure if this is a possible bug or a configuration issue and i have searched and not found anything relevant, anyway i have drupal 4.6 and pathauto (i tried the cvs version of pathauto and got the same result) i have the path module and pathauto setup and working with the following patterns;

[vocab]/[catpath]/[title].html
[vocab]/[catpath].html
user/[user].html

So if i do a bulk update pathauto goes and generates all these lovely seo urls which is great, the problem occurs when i go back in and edit a piece of content after the bulk update, so i click edit and can see in the path alias windows the correct url e.g. "category/term/pagetitle.html" but when i click submit it gets changed to just "pagetitle.html" - any ideas?