Wrong or missing hooks after restore 7.14.1 Omnibus

I've just had a bit of an epic saga upgrading from a Bitnami (now that was a huge mistake) Gitlab 6.5.x image to 7.14.1

Long story short - at the last hurdle I've tried to restore my upgraded backup onto a new server running an Omnibus 7.14.1 version of Gitlab and when I go to call:

sudo gitlab-rake gitlab:check SANITIZE=true

I get the following errors/warnings:

hooks directories in repos are links: ... 
4/1 ... wrong or missing hooks
  Try fixing it:
  sudo -u git -H /opt/gitlab/embedded/service/gitlab-shell//bin/create-hooks
  Check the hooks_path in config/gitlab.yml
  Check your gitlab-shell installation
  For more information see:
  doc/install/installation.md in section "GitLab Shell"
  Please fix the error above and rerun the checks.
4/3 ... wrong or missing hooks
  Try fixing it:
  sudo -u git -H /opt/gitlab/embedded/service/gitlab-shell//bin/create-hooks
  Check the hooks_path in config/gitlab.yml
  Check your gitlab-shell installation
  For more information see:
  doc/install/installation.md in section "GitLab Shell"
  Please fix the error above and rerun the checks.
4/4 ... wrong or missing hooks
  Try fixing it:
  sudo -u git -H /opt/gitlab/embedded/service/gitlab-shell//bin/create-hooks
  Check the hooks_path in config/gitlab.yml
  Check your gitlab-shell installation
  For more information see:
  doc/install/installation.md in section "GitLab Shell"
  Please fix the error above and rerun the checks.
4/6 ... wrong or missing hooks
  Try fixing it:
  sudo -u git -H /opt/gitlab/embedded/service/gitlab-shell//bin/create-hooks
  Check the hooks_path in config/gitlab.yml
  Check your gitlab-shell installation
  For more information see:
  doc/install/installation.md in section "GitLab Shell"
  Please fix the error above and rerun the checks.
9/7 ... wrong or missing hooks
  Try fixing it:
  sudo -u git -H /opt/gitlab/embedded/service/gitlab-shell//bin/create-hooks
  Check the hooks_path in config/gitlab.yml
  Check your gitlab-shell installation
  For more information see:
  doc/install/installation.md in section "GitLab Shell"
  Please fix the error above and rerun the checks.
Running /opt/gitlab/embedded/service/gitlab-shell/bin/check

Everything else checks out ok.

Calling sudo -u git -H /opt/gitlab/embedded/service/gitlab-shell//bin/create-hooks as suggested doesn't seem to do anything and I've not modified config/gitlab.yml from default (or rather the .rb that creates it).

I also don't know if this is an actual issue as my repo's seem to be ok, and projects are showing up in the web interface fine. I just don't want to carry on as is if it's a genuine issue and bites me in the ass later.

Any help would be appreciated.

-Hobsie