For other who are seeing this issue: 'gitlab-ctl reconfigure && gitlab-ctl restart' should resolve this problem without a need to reboot the machine.
The problem is tracked in https://gitlab.com/gitlab-org/gitlab-ce/issues/29855
I rebooted de entire machine and it is working now
``` Running with gitlab-ci-multi-runner 9.0.0[...] Cloning repository... Cloning into '/builds/xxxxxxx'... warning: You appear to have cloned an empty repository. Checking out xxxxxxx as master... fatal: reference is not a tree: xxxxxx ```