I can't say for sure because i dont know how the background music playback works but if it uses the VLC player then maybe nobody has figured this out yet because its an issue with the way VLC is used to play the files. Maybe the part of the script that calls on VLC codec to play the audio file can only handle one file at a time and thats why the first file is the only one thats shuffled. In the GUI you set up a playlist first then shuffle is toggled and all the files are randomized. My guess is that whatever big box is using isnt considering all the files in the background root and shuffling them that way because it also has to adhere to the subfolder structure for platform specific music.
If all this is the case then im sure the reason it hasnt been dealt with is that it would involve rewriting the shuffle script which would maybe break the platform specific option. Easiest solution imo would be to incorporate playlist functionality. Like just drop a .m3u or .plx file in the background folder which points to audio files in any folder and use that playlist to shuffle the files.
Of course all of this is speculative and like i said i dont know if thats even how it works but either way using playlist files sounds good in theory right?