Permission denied with shell when running with gitlab-runner start, working with gitlab-runner run

I'm running Ubuntu 14.04 LTS with Gitlab CI Multi Runner v0.6.2 This is my .gitlab-ci.yml :

staging:
  type: deploy
  script:
  - apt-get update -qy
  - apt-get install -y nodejs
  - npm install -d
  only:
  - master

production:
  type: deploy
  script:
  - apt-get update -qy
  - apt-get install -y nodejs
  - npm install -d
  only:
  - tags

and my /etc/gitlab-runner/config.toml

concurrent = 1

[[runners]]
  url = "URL_GOES_HERE"
  token = "TOKEN_GOES_HERE"
  name = "RUNNER_NAME"
  executor = "shell"
  shell = "bash"
  privileged = true
  [runners.ssh]
  [runners.docker]
    image = ""
    privileged = false
  [runners.parallels]
    base_name = ""

When I start the CI with gitlab-runner start as root, running commands such as apt-get update -qy gives me a Permission denied error, which results in the following message:

ERROR: Build failed with: exit status 1

When I start the runner with gitlab-runner run, though, (both with --debug and without it) everything runs perfectly.

I already have added the gitlab-runner user to the root group and sudoers file, but without any results.