Andrew,
I know you are frustrated but I am not aware of any problems like this so please bare with us, this is a new problem that seems unique to you and your system.
OK, you have not wasted the hours, file them manually while we try and sort the problem out....
Next, please can you give me a little detail about the flights.... flight Number, Departure, Destination and Aircraft as well as any other details you can tell me.
As Sotiris says, this problem could be to do with you starting the flogger with the engines running or taxiing too fast, please can you give us a brief rundown of how you start the flogger and your flight.
We will try and solve this for you as fast as we can although I am still at work and Bruno is away for a while so it make take a while.