Chrome content script not executing on Ember site

I've got an Google Chrome extension which has the following content script syntax in it's manifest.json:

  "content_scripts": [
    {
      "matches": [
                    "https://example.com/*"
                  ],
      "js": ["js/jquery-2.1.1.js", "js/custom.js"],
      "run_at": "document_end",
      "all_frames": true
    }
  ],

When testing this extension on an Ember site, it runs on initial page load but after changing the page, it does not get injected again.

For non-Ember users, Ember can update the URL and page content without performing an entire page reload which appears to be causing this issue.

Is anyone aware of a work-around for examples like this?