Background: During an investigation the FAA discovered that crewmembers who had the simple habit of placing their shoe on the footrest just below the instrument panel could inadvertently put the ATC transponder into standby mode, or change radio frequencies without the crew's awareness. Further, they found that pilots might not notice the corresponding indication on the Pilot Flight Display due to the white colored letters, which are not as noticeable as differently colored caution or warning indications.
One of the sub-plots in the drama ensuing from the Gol-Embraer collision is the possibility of direct criminal charges against the Embraer crew and the ensuing arguments about whether or not the pilots should return to Brazilian jurisdiction to provide further testimony, or to submit to trial as criminal defendants.
The post-accident investigative process in Brazil has been marred by conspicuous public confusion of political, military, corporate and personal interests in 'spinning' facts, coloring details, broadcasting unsubstantiated accusations and meddling with the methods of investigation. Few serious observers - with access to information made public - would imagine the investigations have been either fair or thorough.
Under such circumstances, one can see some reason for concern on the part of the pilots that they might be caught in the middle of a political show trial, with objectives other than fairness and fact-finding.
One can also note that the referenced FAA advisory circular, inconspicuous as it is, creates an official standard of plausible deniability for the Embraer crew, in regard to the primary allegation floated about in Brazil - that the crew intentionally disabled the transponder for unspecified reasons. Presumably the FAA kept good notes on the instances and sources indicating the inadvertent shutoff problem they describe in their official circular, so the net effect is to create a strong affirmative defence for any and all claims related to the Embraer crew responsibility for the transponder outage that may have been a factor in the aerial collision.
Certain facts clarified, plot thickens.