I think this is a playback issue, where MC thinks it can play a track because it meets the basic requirements, but there is something a little different about the track that means the DLNA Renderer can't play it. That is why playback progresses in MC, but nothing is actually heard. So I don't think the DLNA Controller Options will make a difference.
It is very common for DLNA Renderers built into hardware like Network Streamers to be far less capable than the built-in player, in terms of formats that they will play. In fact, the User Manual of the Sony Media Player SMP-N200 very explicitly says some formats can be played (via the HDMI or other inputs), but not if they are played from a DLNA Server.
For example, the SMP-N200 can't play AAC/HE-AAC or WMA9 Standard if played via DLNA, as per note 2 on page 27: *2 The player does not play this file format on a DLNA server.
However, it does play the LPCM format in WAV files, which is Linear PCM with a Header, and that is what the MC "PCM 16-bit" format is. Hence I expected forcing transcoding to the "PCM 16-bit" format using the "Specified output format" Audio Mode would make the problem files play successfully.
Do the FLAC files that won't play have different Sample Rates or Bit Depths to those that play?Try adding a Sample Rate adjustment to the DLNA DSP settings, and see if resampling the format makes it playable. See the first attached image.
You should also be able to see some contents in the Audio Path if you resample to a new Sample Rate. However, this feature is a bit new, and in my testing so far it doesn't always populate the Audio Path dialogue. One way that definitely does is to swap the left and right channels using the Parametric Equaliser. See this post, and the associated thread, to see how to go about that:
https://yabb.jriver.com/interact/index.php/topic,124884.msg865611.html#msg865611 See the second image for what I have done.
Naturally, all this is just to work out the problem, and isn't permanent.
Oh, my other thought was if you were using ZoneSwitch, maybe something in those specific files switches MC to another Zone, which isn't connected to anything and hence no sounds can be heard. But I see that you only have the Player and Media Player Zones, so it is unlikely to be that. You don't have ZoneSwitch turned on, do you?