Adding a TV show episode as a MKV file everything works fine, metadata will be downloaded and episode title is correct.
If I add the same episode as an MP4 file (ffmpeg direct copy of streams) the title will not be downloaded correctly (it seems to be used from MP4 internal title metadata instead).
By the way I use MP4 because it is working with plexconnect and ATV in direct play mode and 5.1 sound.
That’'s a pretty good question. Plex punishes users of MP4/M4V files for some reason and to further this punishment they also put Local Media Assets into the top slot in the Agent Lists (prefers bogus embedded titles over everything else) so there’s almost no escape from the beatings Plex is dealing out on us… almost no escape.
Drag Local Media Assets to the bottom of every Agent list you have. Enabled, but Demoted. You’ll still be able to use the functions LMA provides, but it won’t give tip-top priority to Title Fields.
I’ve been doing deep-cavity searches on my media around here for some time sweeping all files clean. It’s just part of the process, but sometimes one sneaks through. My LMA is at the bottom so it’s no big deal until I find it on a spot check and have to ‘Glove Up’!
(and I use those ‘Cow Gloves’ that go right up to my armpits - when we go, we go deep)

If you are using Windows and have a true MP4/M4V file, you can right-click the file goto properties --> details --> remove properties and personal information
You can do this on multiple files at a time. I did over 600 files at once and it completed in about 4 minutes.