Since it's happening without Codekit as a factor, you may have something odd in your config.rb file. In the root directory of your project (probably the directory that contains the css and sass directories), open the file config.rb in your text editor (Sublime Text). Look for these lines:
css_dir = something
sass_dir = something
These lines tell Sass where to put the resulting files. It sounds like you want it like this:
css_dir = "css"
sass_dir = "sass"