I was having the same issue for a couple days on a custom PCB with an ATMEGA2560 chip on it. After trying many different things, re-installing the FTDI drivers fixed the problem for me.
I think that when I started using those cheap Chinese Arduinos, the ones with the CH430 USB to serial converter IC, the drivers for the CH430 conflicted with the drivers for the FTDI chip. Also, upgrading my OS could have caused the FTDI drivers to stop working as well, though I am not sure.
I hope this works for you guys!