When building paths, they are reversed in the bundle output - so the dependency in the bundle output will be via System.register("some_js_file", ...) and not System.register("some_path/some_js_file.js", ...
In order for the normalizations to work out correctly it's important the paths configuration is present in the production environment before the bundle itself is loaded.
To debug bundling carefully try inspecting `Object.keys(System.defined)` to see what modules have been defined by the bundle, and why they aren't matching up with `System.normalizeSync('some_js_file')`.