I am encountering the exact same issue as http://wordpress.org/support/topic/search-terms-erroneously-returning-zero-posts?replies=6. It is on Multisite. I have activated both for the individual site and network wide, deactivated/reactivated, etc. When I look at the relevanssi db table I can see the search terms, I see it in the logs, the db looks ok however it does not show up on the search results page.
I tried var_dumping everything I could find listed in other helpful posts, but it always resulted in an empty array.
I also tried both logged in and out with the same results. Multiple browsers to catch and caching