Mod randomly says "stage altered, rebuilding" when nothing about the stage has changed

[liamAJ2016]

At a random point in the song (usually multiple times and close to the start), the mod will stop and say the stage was altered and replace one of the noteblocks on the corners however the stage was not changed in any way

[Sk8kman]

That's because your noteblocks are placed above grass blocks. When the grass eventually turns to dirt, it updates the noteblock to be the "harp" instrument, thus causing SongPlayer to need to rebuild the noteblock with the proper instrument again.