I have followed the documentation to manually setup the webhooks at https://support.cloudbees.com/hc/en-us/articles/224543927-GitHub-webhook-configuration but my multi-branch pipeline jobs never get triggered. I've had to switch to using the standard git plugin to trigger the multi-branch pipeline jobs but that has less functionality than the GitHub branch source plugin (i.e. no pull requests). I haven't had any issues with webhooks from GitHub Enterprise on the standard pipeline jobs, just the multi-branch pipeline jobs.