Furia is not correct in that the pilots activating the flaps handle is an established fact, confused probably by all the press reports (in Spain at least) that flat-out refuse to speak of even the possibility of human error but of "flaps failure". Nowhere there are indications about that. Of course you can read the CIAIAC report yourself here:
Preliminary report A-032/2008 - CIAIAC - Ministerio de Fomento
Indeed CIAIAC preliminary report point to the pilots, PERHAPS, going over the required checklist items and calling them ("ok"). Although PERHAPS not 100% according to regulations, but pretty close in the worst case, unofficially. The report doesn't say the CVR confirms the handles down (i.e. a noise is heard as it goes down) nor does the FDR have a way (
AFAIK) of knowing the actual handle position (only the position of the flaps and slats, if working properly).
The flaps were down 11º on the first takeoff "attempt", but not on the second according to the FDR. The report states that the slats weren't likely out either (from recovered wreckage evidence), but CIAIAC lacks the confirmation by the FDR because it wasn't working quite right for the selected flight computer #2. Perhaps the QAR can "confirm" that now.
Regardless, the symptoms of the airplane stalling seem more consistent with a flaps and slats "deployment failure" than with only flaps, although both scenarios are possible, of course.
The report also says that they are trying to establish the procedures to try to determine the position of the flaps handle at the time of take-off. Nothing else.
The TOCWS, indeed, seems to have failed, as the configuration was incorrect (at least for the flaps) and the alarm didn't sound.
While we all still give the benefit of the doubt as to whether the flaps handle was lowered and both flaps and slats on both wings failed to deploy while the indicators for the slats properly lighted to the TAKEOFF position (while the rest of the lights remained off) and the analog dial indicators for both flaps signaled the correct 11º position, we all know that it is basically imposible and it is far more likely that the handle was never lowered, as it has happened many times before like in Nortwest, Delta, LAPA or MAP cases. Or, at least, even if it was lowered, that the indicators were never checked to be in the correct position. Either way, it would be a crew error. This action would've been carried out by the copilot in this case, rather than the pilot, it seems.
Also, the pilots noticing the RAT probe heater turned on came way late in the line up taxi roll for the first "takeoff attempt", pointing to probably having gone unnoticed until the temperature tripped over 99º, firing an autothrottle warning, rather than by reading the amp meter for the heater or doing a sanity RAT indication check early on, perhaps. I don't know if the SOP required such a test, but it wouldn't have been a bad idea that the crew checked the stuff anyway.