When reading feeds from Google in the Google Reader, and then updating the gategory the feed is located in, it is still marked as unread.
If you mark the feed and select Update, the status of the posts gets updated.
How to reproduce:
1: Create a category in Google Reader and add a feed to it.
2: Connect RSS Bandit to your Google feeds.
(Now it should show the category with the feed in, hopefully with some unread posts).
3: Read some of the posts in Google Reader.
4: In RSS Bandit, right click on the category and select Update.
Note how the posts are still marked as unread.
Instead of clicking Update on the category, do it on every feed, since it works if you do it there.
I'm using the 184.108.40.2060 build.