Your APM settings seem to be Ok. As I never used a gentwire cable before, let's try to diagnose what it's doing.
Please connect the gentwire directly to the RC receiver channels 3 (throttle) and 2 (pitch), without using the pixhawk. Download the GentWire test script from
http://www.gentles.ltd.uk/gentwire/chdk_sdm/CHDK2Tester.zip, run the script and report back (instructions for the script are at
http://www.gentles.ltd.uk/gentwire/chdk_sdm/index.htm). Does the camera report "channel 1 up" when you move the throttle all the way up, "channel 1 middle" when you move the throttle to the middle, "channel 1 down" when you move the throttle down? Do the same with the pitch stick. It should report the same, but with channel 2. Does the script report your actions correctly?
What happens when you connect only one cable to the channel 3 (throttle)? What does the test script report?
Next, modify the test script:
Replace lines 13 to 19 (all the lines that start with "if a ....") with just a single line: "print a" (without the quote marks).
Save the script, and run it while testing every combination of the throttle & pitch positions (ie: throttle down & pitch down; next throttle down & pitch center; next throttle down & pitch up; then throttle middle & pitch down; etc). What does the script report for every combination? You could also test what the script reports when you only connect one cable to the throttle, and leave the other cable disconnected from the pitch.
