That's really weird. Sound's like a faulty connection. If you know how to take apart the board and are comfortable with dealing with fine electronics then take a look at some You Tube videos and try to see if there is a physical problem. It could be, and could just require very minor soldering that would take less than 5 minutes, albeit it is rarely the case.
So the Fn key, when it doesn't work, doesn't work at all? Not even with any of the other keys? Also, keep the keyboard in reactive mode if possible, when you can get it working again. Check to see if you still get LED light when you depress key if it doesnt work, which means that there is current flowing, which could mean that there is an internal circuit or chip issue. I'm not too sure though, you should go talk to some Ducky Channel reps.