Attached is a LV8.5 VI I wrote to do basically what you want to do. You would use this VI in your make EXE.
It basically opens an ActiveX reference to LabVIEW, and runs the BuildTargetBuildSpecification.vi provided by NI to programatically build a project item. Since the VI runs in the LabVIEW development environment, you will not get the errors associated with trying to build in the runtime engine.
This still requires the LabVIEW Development System to be installed on the PC as well as the Application Builder. It does not require LabVIEW to be open at the time the VI is called, nor does it require it to be closed. The example NI provides will only run in the LabVIEW Development System and requires LabVIEW to be closed in order to handle command line arguments.
Brief Instructions:
The VI has three states: Init, Build, Close.
Init opens an ActiveX reference to LabVIEW and opens the BuildTargetBuildSpecification.vi reference.
Build builds an item in a project.
Close, closes the VI and ActiveX references.