Case # 824400 (for some reason the fogbugz page for this never loads when I try to view my bug report)
In 5.4.0, when you build a Windows 8.1 Universal project, the solution Unity generates has broken references to DLLs specified for SDK81 and PhoneSDK81. The DLLs are properly copied into the solution, but the references in both the Windows 8.1 and the Windows 8.1 Phone projects are broken. The solution is to delete the references and link them yourself to the ones copied to the solution. The locations are as follows:
Windows 8.1 project:
MainFolder\Project_Name\Project_Name.Windows\Plugins\SDK81\
Windows 8.1 Phone project:
MainFolder\Project_Name\Project_Name.WindowsPhone\Plugins\PhoneSDK81\
This issue does not occur with a Windows 8.1 non-universal build.