I had a similar bug because my Visual Studio Pro is in French. When you install Windows phone SDK, an express version of vs is already installed, you can create phone project in this version and open these projects in vs pro but you cannot create phone project directly in vs pro, that's right ?
Go to : C:\Program Files (x86)\Microsoft Visual Studio 11.0\Common7\IDE\ProjectTemplates\CSharp\Windows Phone
You should have a folder called 1033, it contains phone template for english version of visual studio. Copy and paste it then rename the copy in your code language (http://msdn.microsoft.com/en-us/library/0t12k0f0.aspx , for me it's 1036).
After that, close visual studio, launch C:\Program Files (x86)\Microsoft Visual Studio 11.0\Common7\Tools\VsDevCmd.bat with admin rights and type : devenv.exe /InstallVSTemplates /ResetSettings
Relaunch visual studio pro, and you should have a Windows phone entry.