Drush Omega Guard - "command could not be found" or "could not locate Gemfile"
Answer from the comments above, documented here per Molot's request:

In the case where your settings.php file is not in the 'default' folder, Drush needs you to specify --uri=site_name.com, unless it can determine the site to use via your cwd (e.g. if you have set your working directory to sites/site_name.com, as described in the question).  --uri is not necessary if you have a 'default' site, but it is necessary if you use any other name for your site folder, even if you only have one site in the Drupal installation.

Seems that the problem with finding the Gemfile was resolved by always setting the working directory to the theme directory, where the Gemfile was located.  Doing this while using --uri with Drush solved the problem.