help to understand files in sites/all/default/files/js folder
Like you said these are just cached versions of the javascript files. Drupal compresses them so they can be served to the user faster, notice the difference in file size between the version 29.1 KB opposed to 117.4 KB.

Are there any error when you clear cache through drush? Mostly I've found that they stay behind when you run drush as a user that cannot modify the files, e.g. a user not in whatever group owns the files. In this case you need to add your user to whatever group owns the files.