Just to be clear, the disconnect that sometimes occurs is suspected to be caused by the Pro Controller's firmware, it's not a result of using the program or perhaps even the bluetooth stack. I had already used my Pro Controller with my Wii U so I was unaware that it was an issue, even when I experienced it for the first time I though it was just a fluke since I was experimenting. I've tacked it to the top post now.
But the question is can it detect Pro Controllers and newer WiimotePlus controllers with the Windows Stack. The (probably) firmware of the Pro Controller and newer Wiimotes don't play nice with the Windows BT Stack, so once data is requested the controller disconnects. But it doesn't occur for the other Wiimotes and its peripherals. WiinUPro can still be used with the Windows BT Stack for those devices that will stay connected.