Here are two files. The log from the A3400 configured to use USB Shot Control as OneShot and the A3400 configured to use USB Shot Control as Pixhawk.
A quick look at those logs shows me that both were run in "One Shot" mode. Look for :
Focus:AF Video:0 USB:2:1 Tmo:0in the log. The "USB:2" means one shot mode. Pixhawk mode is "USB:4".
Please post a log file with your A3400 set to pixhawk mode. It would be nice to see the results of taking a couple of test shots too - don't just stop the script and dump the log please. (Logs with both One shot and Pixhawk modes selected please).
In the meantime, I'll find one of my debug scripts that dumps a lot more info to the log file so that we can see if your A3400 CHDK port is possibly buggy.
Also, if you look at
KAP UAV Exposure Control Script : Camera Settings it is strongly suggested that you turn off
Continuous Autofocus and
Servo Autofocus in your camera's Canon menu. In all three logs, you have it turned on. That's most likely not related to your pixhawk problems but could cause other focus related issues later.
edit : my last comment in this post may explain why your A4000 log has entries that say :
Warning:MF enable failed***