PeppyMeter and moOde

[Nutul]

Yes, your is a more efficient solution, but I'd prefer not to convert/duplicate files.

This is not actually converting; it's more fixing-to-standard. It's not even duplicating, if you remove the original files after conversion (I guess you refer to m4a => flac, which I actually do). No loss in conversion, although m4a files are generally slightly smaller than the equivalent flac.

Above all, I'm curious to understand what's happened to MPD and if there's a "software-side way" to fix the issue.

This IS a software way... nevertheless, if MPD complains only when PeppyMeters are involved, we may understand from @fdealexa how the stream is read, manipulated (as it clearly appears to be something MPD is complaining...) and output back to MPD.
I think that it may be either of:

1. something peppymeters don't do properly (hence corrupting the stream)
2. something weird in the stream itself, and peppymeters discarding some (for it) unnecessary information without fixing data elsewhere (if required) and rendering the stream valid, but not in its entirety (and MPD being very picky at formats...)

See what Francesco has to say, as I may be completely on the wrong path with my assumptions.