I refactored the python scripts in Emscripten to make them more sane. There is one difference in how Emscripten is used: If ~/.emscripten does not exist, it will copy tests/settings.py to ~/.emscripten, at which point you would edit the paths etc. in ~/.emscripten - not in tests/settings.py, which is how things were before (and that was bad).
If you already have a file at ~/.emscripten, and you probably do if you already ran Emscripten in the past, then that file will not contain all the necessary information. The simplest thing is for you to copy your edited tests/settings.py into ~/.emscripten. Or, you can delete ~/.emscripten and run the tests (python tests/runner.py), which will copy tests/settings.py for you into ~/.emscripten (but remember to change the paths, if you need to).
Sorry for the inconvenience, but the previous way things were was just a hack, which had to be fixed.
Wiki pages on the project site have been updated.