I am using WP 3.8.1 with theme Twenty Fourteen.
I disabled SE for categories, post_tags, pages, and users, leaving it active only for posts.
Settings for archives, feeds, front/home and searches are all on "exclude".
When I select specific posts for exclusion, it works OK for archives and searches (I didn't tried feeds, sorry), but it doesn't exclude them from front/home.
Tried "Main Loop Only" and "All Loops", same result.