Hi AllynH,
I ended up borrowing an oscilloscope to ensure I'm sending at the right frequency. Basically confirming SpiderKenny's comment "I think this is indicative of the non-deterministic nature of GPIO Timing on Galileo (any every other OS based system)." Even though I turn off interrupts it still shifts around quite a bit. There's no way to get a stable frequency like the Arduino. Looking at the oscilloscope, constantly writing HIGH's and LOW's seem to introduce greater noise as well as more shifts in the frequency. What I've found was that using fastGpioDigitalWrite(GPIO_FAST_IO3, HIGH/LOW) with a simdelay function of 12 microseconds (which I based off of the response from DinoT_Intelin this post: pulseIn ) seemed to be most stable. But even then, it did not work consistently. The workaround I applied was basically send the signal multiple times over a very short period of time. Testing with my setup, this worked 99% of the time. Your posts were super helpful in terms of understanding the I/O issues for Galileo, so many thanks to you!