I updated the plugin with wp 1.4.2.
I have a category with NOINDEX set in this plugin. I updated the plugin and made a pagesource of the the category page, but the noindex tag wasn't there anymore.
I checked the category in wp and the noindex was there. I saved the category and checked again with pagesource and the category was finally right with noindex in it.
So you have to save again your categories with noindex when you update this plugin.