Well, if BAe's (or whoever it was at the time) engineers are so good at software, why has a whole fleet of Chinooks been sitting in a hangar unable to fly? As I recall, these were bought without the manufacturers software because "our boys" were going to write their own! The result? They never even got off the ground!
In a big helicopter like a Chinook, if the engines over-speed, the first thing that happens is that the rotor blades fly off, due to the excessive centrifugal force! This is not an optimum flying configuration! So at the first sign of an engine run-away, a helicopter pilot will pull more pitch on the blades to try and absorb the power. So, no, the engines won't show any sign of over-speeding, presumably because the pilots took the correct action to prevent it!
Of course, the result of pulling on more pitch like that is a violent climb, which *could* be interpreted as a desperate attempt to clear rising ground ahead. It could equally be an attempt to stop the blades flying off due to an un-commanded power increase - something which appeared to have been a regular feature during flight tests using that software!
The fact is that we are unlikely to know for sure which it was. What we DO know is that the RAF broke its own procedures in blaming the pilots when there were plenty of other explanations available.
Of course, its very difficult for the dead to defend themselves. Perhaps that's one reason why this story refuses to lie down......