[wizardknight]

829 movies
89 tvshows (4,486 episodes)

All my media is accessed over nfs:// from a remote FreeNAS server.

I'm using MySQL Server 5.5.21.

Reading your post gave me an idea. I converted my setup from SMB to NFS, and the issue of viewed media appearing when it shouldn't resolved.
I would love to know if you used a mysql database and SMB instead of NFS, if you see the odd behavior.

I am speculating that there might be something slightly amiss with the way kodi accesses SMB shares.
I don't think it is OS specific as I have seen the issue on Ubuntu, liberelec, and coreeelec. 

Seems I spoke too soon. After entering and exiting the Movies section several times, the issue returned.