That’s the reason for the inconsistency, yes.
Usually when we investigate these, I find myself agreeing with the Linux decoder about what is/isn’t corrupt.
IIRC, the Windows decoder also accepts some non-mp3 files with an mp3 extension too. These aren’t officially in Roon’s support envelope, but there isn’t a straightforward way for us to exclude them if the “Windows MP3 Codec” accepts them.