In the FAQ:
I've excluded a Page via the plugin but it still shows up in my sidebar when wp_list_pages is called. Why?
At the time (version 1.6.1) the plugin only effects Pages included in the traditional Search feature on a site. It does not trap all selections of Pages via other internal WordPress functions...yet!
I'm trying to exclude categories so that they don't appear on the main page blog, but in asides or sideposts only. This seems to work with the current version, and I think that should remain an option in future upgrades.