Pathauto ignoring [vocab]/[catpath] when creating alias

I am experiencing an issue similar to http://drupal.org/node/23727 when trying to make pathauto automatically produce the following for each article I write: [vocab]/[catpath]/[title]. I noticed there were some changes made a couple of days ago for that issue but am not aware how to download them.

I have checked my pathauto settings about 10 times and they look ok. Every time I submit an article my alias only includes the title of the article eventhough I specified the category and term before submitting. I then have to do a bulk update for all "node path settings" and "category path settings" with "Create a new alias, replacing the old one". The other option is to do a manual edit for each article after its creation to update the alias.

I don't mind doing the above myself but it would be disastrous if several unversed users are submitting articles and they try to do such a thing. Plus once the database starts growing doing bulk updates is worrying for pages already ranked in search engines if I change a parameter and it changes all urls. Please advice if this is a bug or if there is a process I am not familiar with to automate getting the alias [vocab]/[catpath]/[title] as soon as the article is submitted into the system.