Just open up a Visual Studio 2005 command prompt (an easy way of setting up the correct path and enviromental variables), navigate to the project directory, and type: msbuild yourapp.sln. This is NOT dependent on Visual Studio, since MSBuild is actually part of the .NET Framework redistributable package.
When I run this wixproj under msbuild the DefineConstants are NOT included on the command line to candle. I have verified that the IntermediateOutputPath is processed. That was it. I was building our solution including a similar, previous wixproj that did not require the DefineConstants. I am at a dead end. I do not know what to do.