Cannot clone git repo using GitLab CI runners token after update to 10.1.0

Facing issues cloning project after Gitlab upgrade to 10.1.0. Please find log below.

Running with gitlab-runner 10.1.0 (96b34cc)
  on a-dummy-project (dbbc5126)
Using Docker executor with image a-dummy-image...
Using docker image sha256:f262efcc231129a4ff2231bc2540408b00cefa2265ec3e268ecd4af6911af716 for predefined container...
Using locally found image version due to if-not-present pull policy
Using docker image oaksnode ID=sha256:1b5419dcad52a6aa6e8d987c12cfbe1d91d73dc487cb1ebf8d8d91dce611a722 for build container...
Running on runner-dbbc5126-project-1224-concurrent-0 via ip-172-31-4-118...
Cloning repository...
Cloning into '/builds/html-design/project'...
fatal: unable to access 'http://gitlab-ci-token:xxxxxxxxxxxxxxxxxxxx@git.mycompany.com/project/url.git/': The requested URL returned error: 403
ERROR: Job failed: exit code 1

I've just re-registered the runner believing if this could solve the issue.

My runner version info is as below.

ubuntu@ip-172-31-4-118:~$ gitlab-runner -v
Version:      10.1.0
Git revision: c1ecf97f
Git branch:   10-1-stable
GO version:   go1.8.3
Built:        Sat, 21 Oct 2017 21:33:24 +0000
OS/Arch:      linux/amd64

Setting Enabled Git access protocols is set to Use both SSH and HTTP(S).

Manual clone returns below error:

ubuntu@ip-172-31-4-118:~$ git clone http://gitlab-ci-token:<gitlab-ci-token>@git.example.com/prject/url.git
Cloning into 'oaks-frontend'...
remote: HTTP Basic: Access denied
fatal: Authentication failed for 'http://gitlab-ci-token:<gitlab-ci-token>@git.example.com/project/url.git/'

Please help, all of my pipelines are failing because of this issue. Is there a straightforward way to downgrade Gitlab?