I don't think it's the controller's fault because I have two and it still does it with any of the two.
I can't live with this because I buy a lot of digital games and my connection is too crap. I need the ~12 GB I can download every night
Agreed, it's NOT the controllers - the console is crashing as it shuts down and breaking the link with the controller.
I've just done something quite telling not 5 mins ago, basically my console has been off in instant on mode all day and has been downloading FIFA 17, I've been at home today so every hour or so I've been turning the console on using the controller and checking it's % of FIFA download is rising and it is and all is fine, I have then shut down the console using the controller and it works then an hour or so later done the same thing all over again ... No problems - the controller has powered on and powered off the machine EVERY time no faults.
Now 5 mins ago I powered on console again with controller and PAUSED the FIFA download as family home now and people want to use the internet etc.
Now this time when I powered off the console with download PAUSED in queue, the console made TWO shutdown chimes a couple of seconds apart (this is it telling us that it's crashed I think) and the machine shuts down but the controller continues to flash intermittently for a good 2 mins after machine has shutdown.
Once the light on controller stops flashing I press it and lo and behold the machine doesn't come on, So I press console power button and it boots up but NOT in instant on mode - it's the full boot process.
So in theory my machine has been fine all day until I paused a download and shutdown in instant on mode and 2 audible shutdown beeps and blinking controller light after machine went off.
I've now restarted FIFA download to test and now controller shutdown machine with only 1 beep and no flashing after and I am able to start machine again using controller and it's back to instant load to dashboard ...
So basically I'm seeing that as PAUSED downloads in queue are causing the problem at least for me ???
Perhaps you could test same parameters and see what happens at your end ?
HTH