After running the toolkit installer for wix:
For Wix 3.8 and 3.9, with Visual Studio 2012 and 2013, I was required to delete all the cache files in:
"%appdata%..\Local\Microsoft\VisualStudio\11.0\ComponentModelCache"
(for VS 2012) and
"%appdata%..\Local\Microsoft\VisualStudio\12.0\ComponentModelCache"
(for VS 2013) respectively.
After deleting these files, execute from command prompt for each version of VS:
devenv /setup
e.g. "C:\Program Files (x86)\Microsoft Visual Studio 12.0\Common7\IDE\devenv /setup"
and "C:\Program Files (x86)\Microsoft Visual Studio 11.0\Common7\IDE\devenv /setup"
Only after I deleted these files and restarted the machine did executing "devenv /setup" have the desired effect.
If these cache files are not deleted first, then you may experience a problem where your packages fail to load properly. You will know if your packages fail to load because VS will fail miserably upon startup.