Interesting article.
http://www1.folha.uol.com.br/folha/c...5u126678.shtml
To summarize, the investigating authorities are working on a theory that as a brand new airplane, the transponder may have had a "bad electrical contact" with a switch or wiring, meaning that the transponder was on and off (intermittent) without the pilots knowing about it (a possible "infant mortality" issue I suggested earlier). In the article, the sources did not indicate why they were looking at this theory, or what lead them to pursue this theory.
In their "combination of causal events" hypothesis, the pilot did not descend to FL360 from FL370 as per the flight plan, and since the transponder was not working properly due to the "bad contact" problem, the TCAS warning failed. Then after the impact, the "bad contact" corrected due to the impact and turned the transponder back on again. In the article there's some discussion about ATC response to the transponder disappearing prior to the collision, but the computer translation leaves the grammer and exact meaing of that paragraph in doubt (at least for me). I can't tell if ATC tried to contact the Legacy pilots about the loss of the transponder or failed to do so.
In any event according to the article, the authorities are not sure if this is a good theory or not, but are working it as part of the investigation. At least it's nice to know the Aeronautical Authorities are trying to give the pilots the benefit of the doubt about the operation of the transponder.