The S3 wasn't the only bug (though not everyone had the wrong S3 disc).
According to TheDigitalBits.com:
Just to be precise, the 1978 Superman theatrical edition disc (Disc One of the Ultimate Collector's Edition) is supposed to have the revised 5.1 audio (edited down from the 2001 Extended Edition's 5.1 remix) and the ORIGINAL THEATRICAL 2.0 audio. That's what the corrected discs will contain (right now, the 2.0 is the remix also rather than the original theatrical audio).