Yes. This plugin affects only post content. For widgets, it cannot be done because it cannot. Please read this:
http://wordpress.stackexchange.com/questions/10344/how-to-add-a-filter-to-all-widget-output
To make links in menu nofollow, please use this:
http://codex.ww.wp.xz.cn/Defining_Relationships_with_XFN
In menu screen, open Screen Options and check Link Relationship (XFN), and set this field is nofollow in each your menu link.
This isn’t working for me either… meaning that it suddenly conflicts with my adsense display plugins. Very bizarre, but I deactivated all plugins and one-by-one tried to figure out which one was the culprit and it was this one.
