I know nothing of the hardware, nor software. But, ultimately this will be a TTL-level signal between whatever controller and the laser. Gut feeling is you've got a PWM output on the ardi that is either "wrong" (maybe duty cycle?, or some internal calibration), or the software is mis-configured. If you've got access to a scope I'm be examining the signal to the laser and taking it from there. If you get stuck - I'm local, can offer a second pair of eyes and a scope.