Unity 4.6 final release causing issues with Windows 8.1 metro apps

I have two projects that where working in 4.5 and worked well in the 4.6 beta previews. However since upgrading to the final release of 4.6 I am now having issues that I can't find a solution for.

Project 1....

When compiling I am getting something stupid like can't find file UnityCommon.props, I have gone through removing everything from the project that was releated to Visual Studio and still get this.

Project 2

When compiling this I have started to get Project can't run file explorer...

Unity 4.6 final release causing issues with Windows 8.1 metro apps