I am currently running Logos Bible Software 6.6 SR-2 (6.6.0.0069) on a Mid-2010 MacBook Pro that is running OS X 10.11.
I have encountered a problem with the notes and highlighting feature. Let me explain my workflow as I am highlighting and note taking before I explain the problem.
Workflow Explanation: Usually when I highlight something in a book I also copy and paste the text of the highlighted section into the notes document itself. I will then occasionally add my own thoughts and comments about the quoted section immediately below the pasted text (as bullet points, separate paragraph, etc.).
The Problem: In the past, I was able to copy and paste the highlighted text into the note and Logos would automatically include the bibliographic information into the note. I also appreciated that Logos would automatically turn this bibliographic information into a hyperlink directly back to the copied text in the book. However, now I am experiencing a strange problem where the bibliographic entry no longer automatically changes to a hyperlink. The other strange characteristic of this problem is that it seem to occur intermittently even within the same resource.
For instance, today I was following my typical workflow described above. As I was highlighting, copy and paste-ing, and note taking the vast majority of the automatic bibliographic entries were not hyperlinking automatically. However, after 3 highlights/notes I added one new note, and Logos suddenly included the bibliographic information with a hyperlink.
So I have 4 notes/highlights in the same resource. 3 of the notes/highlights do not have hyperlinked bibliographic entries. 1 of the notes/highlights does have a hyperlinked bibliographic entry.
As near as I can tell, I did not do anything differently between the third and fourth highlight.