In my own experience, what you describe (3 flight batteries equals 75% controller charge) is perfectly normal. I've noticed that each flight will eat about 30% from my RC-1A/B controllers and the RC-N1 loses between 25-30% per IFB.
With the...
You got one of the major problems pegged with your response to the other 'forest flier' thread. GPS... or more to the point: the lack of it.
When you don't get a strong satellite uplink, the drone automatically switches to VPS (Vision...