Archive containing the original file and the outputs for both VLC builds: http://www77.zippyshare.com/v/DjV8sRot/file.html
I tested vlc-3.0.0-20161005-0441-git-win64 against vlc-3.0.0-20161005-0315-git-win32 although it happens on current stable (2.2.4 x64) builds as well.
It sounds like there is some audio aliasing happening on the x64 builds while playing mp3 files, which does not happen on x86 ones. Also from what I've tested it happens only to mp3 files, not to wav. Normally I have output mode set to DirectX, but those files have been generated using "file" audio output. The result is the same distortion.
Tested under Windows 7 x64, if it helps.