Pixhawk related problem ? no response to modes

[AndKe]

I am testing the source while waiting for my jD-IO boards to arrive.

I have a few question while troubleshooting:
It seems it kind of works with Pixhawk:
Without mavlink, I get alternating blinking on left/right.
With mavlink, Left/right stays on.
I think bad GPS, (or other alarm) caused left+right to blink together.
I cold not see different blink at low voltage (what is the expected pattern for that ?)

No modes seem to work, the mode indicating led is mostly on, goes off now and then, but no meaningful pattern change for the 6 modes I've tried.

Would you please describe how the alarms should look, and if you have a theory on why modes do not work, at least on Pixhawk..