I have flown close to 30 different 407's, worked in a Bell Helicopter Service Facility, have seen a millon different weird things, but, NEVER A MYSTERIOUS EXCEEDANCE.
Why do you say the exceedances "couldn't have happened". The ECU records all the parameters at the time of failure, for example what did the N1, MGT, do while the overtorque occured? in the graphs that you downloaded from the ECU, did they move at all??
I have seen several people exceed MGT in cruise flight, for just not paying attention and flying too close to the yellow for too long, so it's not impossible.