We tracked this down to a problem with the line endings in GenerateProjectFiles.bat. The source code zip file generated by GitHub saves text files with Unix-style line endings, which causes problems running the batch file.
We’re working on a proper fix for it, but in the meantime the best workaround would be to follow the instructions for forking your own repository on GitHub instead.
This issue should be resolved now. We added a .gitattributes file to GitHub that forces .bat files to retain their Windows-style line endings when source is downloaded from the zip file. Of course, you can always grab the code using a Git client and it will handle line endings correctly already.