I was having a problem with it only linting (w/ rules) one folder/repo and not the other 2 folder / repos.

I have not idea why this is but I tried moving the config file to next folder up. I changed the sublime configuration as follows to account for this:

{
  "node_path": "/usr/local/bin",
  "node_modules_path": "/usr/local/lib/node_modules",
  "config_file": "/Users/c/top/.eslintrc"
}

top is the folder containing my 3 repos/folders however only 1 is using the rules in my config file.

I am using Sublime with the necessary packages - SublimeLinter, SublimeLinter-eslint, and eslint.

It appears that it is linting the files; it is just not applying the config file rules. Very odd.