Using v4.2.9, I was having a problem with uploading certain files to my server and after a day of trying to figure out what was causing the problem, I finally came to realize that it was because the were text files being uploaded in binary mode (from Windows XP to Linux server).
I would like to suggest you add the following two additional file types to the list for determining automatic ascii mode transfer:
*.js - JavaScript files
*.tpl - Smarty.net template files
Thanks