Interesting results today. I received my new Yourdrino RoboRed board. Testing showed that with the MOSFET installed and running at 5V, the new board would reset itself without the need for using the reset pin and capacitor as required with the old board. Testing also showed that running the fan direct 5V PWM signal both new and old board required the reset pin and capacitor to reset. Testing at 3.3V with the MOSFET,does not required the reset pin and capacitor for both the new or old board. Note that running directly at 3.3V without a MOSFET cannot be performed because the voltage needs to be above 3.8 for the fan to run.
In conclusion I cannot say if I damaged the old board or are they operating on the edge of where they reset by themselves or not, and just a small differences in the boards could be putting one over the edge. But I believe the cap and reset pin is probably prudent to use.