If you also have Visual Studio 2012 installed, did you install VS2012 Update 4? From the requirements notes: “This update requires either Visual Studio 2012 with Update 4 or Visual Studio 2013.”
I have almost the same setup as yours (Windows 8.1 Pro 64bit, VS2012 Pro + Update 4, VS2013 Pro + Update 2 RC), and all WP8 emulators work fine here (all = WP8, WP8 Update 3, WP8.1) .
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