I have exactly the same issue. I contacted with very helpful person from NVIDIA on their forums. He send me new console and I send the old one. They want my console to check what's going on. On NVIDIA forums many European users has got this issue on PRO model. Unfortunately the new model that I received from NVIDIA has this issue to
oddly I had this issue when I first updated (Shield 16GB not rooted) to 3.0 where I had to unplug it and plug it back in to wake it up but it went away after a few days.
the only thing that changed around the time it went away was that I started using adoptive storage with a 64gb sd card but since there isn't much to link the two it was very likely just coincidence that it stopped at that time.
thats probably not much help but I thought I would mention it just in case.