If the value for 'filename' in the 'output' section of a webpack configuration is set to a name that ends in '.jsm', no source map file is stored in the output directory, even if the babel loader is configured with sourceMaps : true.
To reproduce: with a configuration that produces source maps, just change the extension of your output.filename value to '.jsm' and no sourcemap is generated (remember to remove it from your distribution directory first, otherwise you won't notice easily that it isn't saved in the output directory).
I think this is a Webpack issue, not a Babel issue, but before reporting it I would like to know if this is a feature rather than a bug?