I had the similar issue after upgrading to VS 2015 Update 1.
VS was thinking that my run-time version was RC1, but DNVM (.NET Version Manager) had no clue about it. So when I was publishing the solution it was using beta nuget packages, configuration for drop folders, builds and so on.
So what I've done is:
dnvm list
To show me the list of available runtimes. Mine was looking like that:
Active Version Runtime Architecture OperatingSystem Alias
------ ------- ------- ------------ --------------- -----
1.0.0-beta5 clr x64 win
1.0.0-beta5 clr x86 win
1.0.0-beta5 coreclr x64 win
1.0.0-beta5 coreclr x86 win
* 1.0.0-beta7 clr x86 win default
After that I've upgraded DNVM to the latest version via:
dnvm update-self
And installed the latest stable version of runtime:
dnvm upgrade
It will also set the latest runtime as default for your environment. After the upgrade you should get the following version list:
Active Version Runtime Architecture OperatingSystem Alias
------ ------- ------- ------------ --------------- -----
1.0.0-beta5 clr x64 win
1.0.0-beta5 clr x86 win
1.0.0-beta5 coreclr x64 win
1.0.0-beta5 coreclr x86 win
1.0.0-beta7 clr x86 win
1.0.0-rc1-update1 clr x64 win
* 1.0.0-rc1-update1 clr x86 win default
1.0.0-rc1-update1 coreclr x64 win
1.0.0-rc1-update1 coreclr x86 win
Hope that helps.