Pixhawk 2.1 Loiter Drift Problem

We are building a quadcopter using the SpektreWorks carrier board for PixHawk 2.1 Cube and currently facing the problem of drifting away in loiter mode as described below:

1) The quad is installed with firmware version 3.5.0-rc11.
2) In our test flight, it can take off fine and we could control it in stabilize and altitude hold modes.
3) But after switching to loiter, the quad started drifting away slowly but steadily for 15'-20' and we had to switch back to stabilize mode to control its horizontal movement.
4) The GPS was solidly fixed
5) The accelerometer and compass are calibrated well.
6) EFK checked and performed well within limit.
7) Vibration was well within limit.
8) The flight log shows that the velocity X and Y don't track the desired velocity (when not only in loiter mode) so I suspect the problem might be that the default PixHawk PID parameters that we used might not perform up to the3691351466?profile=original

So could you please take a look at the log file and give us your expert advice?
1. Did the problem come from the PixHawk PID parameters?
2. Would an autotune help getting the Loiter parameters (and other controller's parameters) right?
3. If we want to manual tune those parameters, how can we change them to have a better result?

This is the log file: https://www.mediafire.com/file/ch4nufkbez99i79/2017-08-04%2016-17-30.log

Thank you for your time and I appreciate any ideas and support from you guys!

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