I anxiously await a real accident report on this derailment. A look at the pictures, map on google, a few news articles including description of train direction led to many things not making sense.
A summary of the situation: The train was eastbound (outbound from Oakland) between Orinda and Lafayette, and had shortly before left Orinda station. The line in this area is in the median of state highway 24, which appears to be a limited access highway of 4? lanes in each direction. The center of the crossovers shown in the pictures of the derailment is, based on Google Maps, about 2,500 feet, in otherwords, about one-half mile east of the center of Orinda station. Facing eastbound, in consists of one right hand followed by one left hand crossover.
The train is shown with the front car plus the front bogie of the second car on the left track, which would be the normal westbound track. The remainder of the train, including the second bogie on the second car is on the right track, which would be the normal eastbound track. The front of the train is about 150 feet short of the beginning of the first crossover. I do not know the number of the turnout nor the track centers, but the crossover appears to be about 200 feet long.
The conductor rail coverboard was missing between the end of the train and the crossover, with possible other damage to conductor rail system.
Said all that to say this: It appears that the train had been moving west at the time of the derailment. It seems likely that the train was moving east as it was supposed to and stopped about one and one-half car lengths beyond the far switch of the first crossover and then started backing up (i.e. going west) with the crossover set for the crossover move. This seems to be the only reasonable possibility. This is borne out by one of statements given to the SF Chronicle that the train stopped and then began backing up. It is likely that the crossover may have been set against the normal train movement and the train went over the switch in a trailing move. It is common for a train to go over a switch in a trailing move and not derail even though the switch is set against it. This will result in damage to the switch operating mechanisms that must be repaired post haste. The fire was a result of the car body contacting the power rail, shorting out the circuit.
Why these moves were made I don't know. What exactly the operator was told to do and what he did, and whether these were reasonable and appropriate for the situation, again I don't know and for this, I refuse to speculate.