Executing Shell::command( $wgScoreLilyPond, '--version' ) returns score-versionerr with the message:
'c:\LilyPond\usr\bin\lilypond.exe" "--version' is not recognized as an internal or external command, operable program, or batch file.
Notably, the quotation marks are quite odd in the error message. This works under Vagrant though. It only fails on Windows. Extending the issue, this probably also affects the rendering stage.