After upgrading to version 1.15 of MSbuild plugin (from 1.13), it appears that dos style environment variables no longer work in the MSBuild arguments.
Unix style environment variables do appear to work, and provide a workaround.
For example, the following does not work:
MSBuild Build File: %Project%\proj.sln
but this does:
MSBuild Build File: $
I'm not sure if the change was intentional, but if it was, the help pop-ups are incorrect as they say the arguments should be the same as if you were to run MSBuild from the command line. Regardless of the intent, it would probably be good to have an environment variable in the help pop-up example.