I tested this on the latest version of 11x and was unable to replicate this issue. Here is how i attempted:
1.Created a new folder under my root folder
2. Set the new folders setting for 'Include articles in automatic searches' to unchecked
3. Made sure kb search was enabled for live chats
4. waited for the kb article to get indexed
4. went to portal and started a live chat with myself ('typing in some key words to trigger the kb article to show')
6. it did not show my kb article.
7. i went back and turned the setting for 'Include articles in automatic searches' back to checked and started another chat with myself typing in the same key words.
8. the article did show.
If i did not test this correctly give me exact steps and I will try again on my local install.