Hey, my Fan Control PCB has arrived and I successfully installed it in my MegaPi. I love how quiet (Silent? =) ) my pi is now! I observed exactly the same issues as you, too - which makes perfect sense, given the fact we seem to have the same fans. Not a big issue for me though, I will be more than happy with just an on/off script! Also the LED is very bright indeed, but it doesn't shine through the case - I can only see it when I open the SD card storage, which to me is a plus (can debug it visually). Thank you for making me aware of this PCB! It took a very long time to arrive but I am very happy with it, as honestly the buzzing was kinda bothering me when playing GameBoy games or watching movies. EDIT: I am therefore joining the question - does anybody know a fan which would play nice with PWM regulation? This one definitely doesn't like it.

I would like to recommend the following reading, which I have applied to my Raspberry pi https://descubriendolaorangepi.wordpress.com/2017/06/20/gpio-en-c-control-automatico-de-ventilador-segun-la-temperatura/ I usually use this other script in Python https://pastebin.com/EsbQEJzw