I think Tim Vasquez' meteorological analysis posted earlier is a very good read. One of the possible scenarios he mentions is that if it encountered a vigorous updraft in a fledgling cell, of which there were quite a few developing at the time, then it wouldn't show on the radar, as the precip wouldn't have had time to develop yet. To me that seems more pausible than lightning, for what it's worth (ie. absolutely nothing)
Air France 447 - AFR447 - A detailed meteorological analysis - Satellite and weather data