There's still the possiblity that the pilots thought they had the transponder turned on, but there was a switch problem etc, as mentioned previously.
However it would be interesting to know why ATC tried 7 times to contact the Legacy and failed, even though the black box (CVR I assume) recorded the attempts. I don't know how accurate the article is in discribing the events, but the circumstances as discribed don't sound very good. If ATC calls are on the CVR and the pilots failed to respond, that would not be good at all. We'll have to wait for more authoritative details.
Does anyone know if radio communications are problematic in this area (sorry if this has already been discussed, I'm in a hurry to post this, I have a flight to catch)?