Since you have a receiver, it might be better NOT to mess within Audio MIDI unless you absolutely have to--instead let the AVR do the heavy lifting, it's the job of the AVR to handle incoming audio and send the audio you want to your speakers. That's also another way of saying the problem you're experiencing is almost certainly related to something other than AudioMIDI--how well you set up the inputs on your AVR, your connection from the Mini to the AVR, the player you're using to playback the video and even the file itself, especially if you didn't create the file and don't know what kind of audio it contains. Before you try to negotiate within AudioMIDI maybe deal with some easier questions first:
Which model Mini do you have, how are you sending audio from the Mini to the Yamaha and what app are you using to play the video?
What is this file of and what kind of audio does it contain?
Is it only this file that is problematic or are all your video files affected? At this point make sure you're not trying to play a file with high def audio, just use something with basic DD 2.0 or 5.1
You're playing the video file with something, a software player, whatever player you're using, try another one--same issues?
Next poke around in the settings of that app and tell it how you want it to pass audio to the AVR...it's called different things but aim for something called digital pass through--that usually means whatever the audio is it will passed to the AVR untouched--if the audio in the file is DD 5.1 that's how the AVR will see it--the Mini and Audio MIDI will not "process" it--then it is up to the AVR to direct that 5.1 into your 3.1 setup. If you aren't that familiar with your AVR yet that also means you'll have to read the manual to figure out how to set up that input on the Yamaha--with most AVRs you have to setup each audio input, in other words tell the AVR what to look for, what to expect, and what to do with that audio once it sees it. Most AVRs will detect and display what kind of audio it is receiving from the file--is your Yamaha switching and displaying audio correctly as you play different files?
Pvr4Craig is not wrong in suggesting AudioMIDI may be involved, thats one of several places to check settings which could affect you:
1) the master hardware audio settings on the Mini within its OS, that's what's inside Audio MIDI;
2) you have audio settings within each app or software player, like Plex, XMBC/Kodi, VLC et al that control what it does with audio;
3) then there's how you set up the input for the Mini on the AVR.
It's just a guess but my sense is you'll find your answer in 2) or 3) or within the file itself before you have to go changing things in AudioMIDI.