Yun digital-ports seem to behave differently than Uno, but why? (Copter-Project)

Hi all,
i am trying to get a Quadcopter running with an Arduino Yun, based on the multiwii project. I cannot get it to work with the Receiver (Spektrum AR8000) properly, the pwm-signals are not getting through (multiwii config app does not respond when i move the sticks of the rc). I tested the exact same config with an Uno and bars were moving. Then i created a test-sketch to read the RC-Input (with pulseIn()) and control the servos manually with the values (by servo.write()) - values are getting through and motors are spinning - both on the UNO and the Yun. Therefore i assume it should work in general - but why isn't it working when i use the multiwii-sketch? Is there something i should consider on the Yun which i am not seeing? I only use digital Pins, the pwm's for the motors/sensors and the others for the rc-input.
Thanks in advance,
Stephan