When I connect the Watchdog input to one of the GPIO, without any code running, it never triggers...
I tried with Grove pins 1 and 2 up to VDD with and without a 100K resistor. No difference...
On a brand new Raspberry PI 3 Model B+, without any app for watchdog, led never blinks when connected to a Raspberry pin that has an internal pull-down resistor. If I connect to a pin that has an internal pull-up resistor, it triggers every 6 seconds or so.
We tested the WatchDog timer much in the same way you are trying. What is Windows IOT doing to the GPIO? We haven't a clue.
Be methodical in your testing
1) Unplug the inputs to the WatchDog timer. Do the LEDs blink periodically? If so, the watchdog is working. Note the time between blinks
2) Connect up the Pulse output to a GPIO (nothing connected to the inputs) write a program that reads that line and prints out the value. You should see it change whenever the LED blinks.
3) Now connect up a GPIO to the GROVE Pin 1 (yes, you could use the pin headers but then you have to tristate the output) and have it pulse low every 30 seconds. If the time between blinks was longer than 30 seconds, then you should never see it blink.
Thus you can tell the watchdog timer is working.
This is the way we tested the unit!
Make sure you have a common ground between the watchdog timer and your Raspberry Pi. Otherwise nothing will work!
Dr. Shovic's favorite quote is: "You can always trust your Mother, but you can never trust your Ground".