Had the same problem. Actually still have the problem but have a workaround. First of all, make sure you're running the latest version of Joycon Explorer. Any chance you are running the joycon through a usb hub? The problem went away when I plugged it directly into my PC. But since I need to run it through a hub, I made a shortcut to the PRS file and stuck the shortcut in my startup folder (on shortcut, I selected "Run Minimized" so it doesn't popup over CF at startup). Since I always cold boot, it works for me. I don't think the shortcut would do anything from hibernation. However, I believe some people have had success from hibernation by plugging it directly to the PC.
Also, make sure JoyCon is run with elevated rights (run as admin).