My graphs show that when you command zero-throttle (PWM = 1100 for C3 input) the Channel 3 output consistently goes to a value of 1000. This is true at the beginning of your flight log (not on these graphs) and also here at the end.
This tells me that ArduPlane is behaving as expected, and is not the source of your problem.
I just had an idea! I have a plane with an “intellegent” ESC (From Castle Creations, I think) which had a strange issue: the Castle ESC calibrates “zero throttle” to be whatever PWM value is seen at power-on. (Let’s say this was 1100, for example.) However, in a particular situation (details aren’t important) it was possible for me to send a lower value via C3 (say 950, for example) for a short period of time. This caused my “intelligent” ESC to re-calibrate the zero-point of the throttle as this lowest value, The unwanted outcome was that the original value (1100, by example) was NO LONGER a zero-throttle command! (It was something like 5% throttle, making turning off the motor impossible without re-using the special 950 command.)
Could something like this be the source of your problem?