It appears that, when generating the source map for debugging js output, the path to the source file ("sources" property) is using a relative path.
Since it is possible (and often desirable) to send the output outside the workspace/project folder (with js-output argument) it seems to me that the path to the main source file should be an absolute path. Also, the map is named with a .js.map suffix even for a MXML main source file. It should follow the extension of the main source file (.js.map or .mxml.map, depending on the main source file). Nicolas Granon