PPM decoder timer

I just got my Navio+ board. I’m using a Raspberry PI 2 and the 3DR PWM to PPM decoder/encoder. While I tried to check my channels with ArduPlane all seemed fine. When I ran PPM_decoder it nearly destroyed me a servo.

After spending an evening trying to figure out what I did wrong, I found that changing the timer (samplingRate) to 10us made it work. So I wonder, should I just run with 5 or 10 (5us also works) or did I do something wrong?

(I’m using emlid-raspberrypi2-raspbian-rt-20150401.img)