I'm not sure if this is a problem with VS2012 or with SP2013. We restored a reverted vm yesterday, and there were a ton of weird SP2013 problems we had to overcome. Then after we got a site collection up and running at the root of port 80, I opened Visual Studio. None of our projects build because they can't find the Microsoft.SharePoint.dll assembly.
I went into a project and removed the old/bad reference, and tried to re-add it. However Microsoft.SharePoint.dll does not show up when searching Framework assemblies. I did find it when browsing to C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\15\ISAPI. However even when I add the reference from there, the project still does not build. It cannot find SharePoint in the Microsoft namespace.
I ran a repair on VS2012 and installed the SP2013 tools for VS2012, but the issue remains.