I am using Co-authors Plus on a site lots of new custom post types. Your plugin runs its filter across all queries - but 1) assumes that wp_query is the target and 2) assumes all items in the wp_post table are included in the co-authors taxonomy.
This leads to odd results.
I have modified the code to "fix" this. Gist - https://gist.github.com/2636235
Take a look at the posts_where and posts_join filters for the core of my "fix"