It heard the 16:35 Bristol Temple Meads to Southend train was travelling at 59mph on 7 March as it passed the previous signal, set to caution.
When the driver saw the next signal set to danger he fully applied the brakes.
But the inquiry was told there was insufficient distance to bring the train to a halt. No-one was injured.
The RAIB's preliminary examination heard as the train approached the first signal its automatic warning system activated after passing a temporary speed limit beacon.
But the driver did not acknowledge it and the train's automatic brakes activated which should have brought it to a halt.
At this point the driver should have contacted the signaller, according to railway regulations, the inquiry was told.
But the driver and fireman took action to cancel the brake after a short period.
By the time the driver saw the danger signal there was insufficient distance remaining to bring the train to a standstill before it reached the Wootton Bassett junction in Wiltshire.
It stopped past the danger signal on one of the rail crossovers but as the points had already been set there was no damage to the train or tracks.
The investigation found no evidence of any malfunction of the signalling or warning equipment.
No injury, damage or derailing happened as a result of the signal being passed at danger.
A full report is due to be published once the inquiry has concluded.
The RAIB investigates railway accidents and incidents in the UK to improve safety, not to establish blame.
A steam train passed a signal set to danger and overshot a busy junction, a Rail Accident Investigation Branch (RAIB) inquiry has been told.