I am having and issue with Plex Media Server 1.2.0.2838-a68e2fe_amd64 on Ubuntu 16.04 with "Update my Library Automatically" selected.
On content that both my wife and I are interested in watching I run a nightly cron job to make a hard link (from the shared directory) to both our individual directories and then I delete the original file in the shared directory.
I've found that PMS is unable to detect properly the new content in both our individual directories. I have to manually enable a "Plex Media Scanner --scan --section <library#>".
I've seen it detect one of our individual directories, but never both. Manually initializing a scan does detect the media as a work-around.
Normally PMS is very good at catching cases where I make any modifications to the files. In this case it isn't working 100% correctly.