I've had no problem with this. Generally speaking, these issues are related to AVRs (not sure which one you have) not having support for any channel assignments between 2.0 and 5.0 (ie 3.1, 4.0, 4.1 etc.) even though they're in spec and should be supported. This is why I've argued several times for disc-based media like the Quadio Blu-Rays being authored as 5.1 even though there's "empty" channels - they don't increase the file size, but ensure 100% compatibility with every playback device.
I've included a couple of pictures of my audio settings below, you can check and see if yours match - the other option is to use software to "pad" any of your multichannel files that have less than 5.1 channels to 5.1. I personally use
@HomerJAU 's wonderful
Music Media Helper which allows you to do all manner of these kinds of things including adding silent channels, remapping files with swapped channels, file and format conversions, tagging and so much more, and best of all it's free (aside from the human cost on Homer's psyche).
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