This is a known bug that we're all running into with Windows 10 64Bit
Launch the "Developer Command Prompt for VS2015" as Administrator
change the working directory over to "C:\Program Files (x86)\Microsoft IoT"
sn -Vr WindowsIoTCoreWatcher.exe
corflags WindowsIoTCoreWatcher.exe /32BIT+ /FORCE
That'll fix it. However, you do not need this program to run to develop for Windows IoT. This just tells you the IP address of the Pi. If you already know that, you can browse to that IP in a browser window and you'll see options to shutdown, restart, deploy, and a bunch of other things. Visual Studio also just needs the IP address to deploy.
Ping me if you have other questions. I've been slowly working through all this myself
Oh, and here's the bug report that you should go upvote -> https://connect.microsoft.com/windowsem ... ls/1295993