Try add logging as it described in wiki.

On my build server it is attempting to poll with the git executable path set for the node.

Server: Ubuntu 14.04.5 LTS

Node: Windows Server 2008 R2

It tries to poll with "C:\Program Files\Git\bin\git.exe" and returns the error "No such file or directory".

It should be polling with the Default located at "/opt/bitnami/git/bin/git"

This is a rather major issue because it does not allow me to perform gihub polling and use any windows machine as a build node, since my jenkins server is ubuntu.

I seem to be experiencing this issue as well. Running on Ubuntu 16.04 with version 1.27 of the plugin. I have "GitHub hook trigger for GITScm polling" checked off in my target job. I've confirmed that GitHub is successfully pushing to Jenkins from the GitHub UI. In my normal system log, I see:

Aug 03, 2017 9:50:37 PM org.jenkinsci.plugins.github_branch_source.PushGHEventSubscriber onEvent

INFO: Received PUSH for https://github.com/myOrg/myRepo from xxx ⇒ SERVER/github-webhook/

The GitHub hook log says, "Polling has not run yet." I set up my logging recorders as per the wiki and saw:

Aug 03, 2017 10:03:35 PM FINE com.cloudbees.jenkins.GitHubWebHook$1 apply
Calling registerHooks() for jenkins-pipeline-test
Aug 03, 2017 10:03:35 PM INFO org.jenkinsci.plugins.github.webhook.WebhookManager$1 run
GitHub webhooks activated for job jenkins-pipeline-test with [] (events: [PUSH])

I'll note that I created a GithubOrganization job, which then faithfully responded to the PUSH and executed a build. So my configuration appears to be correct!

make sure you are using case sensitive characters in scm config on jenkins. because checkout works anyway, but push notifications not. so if you have myOrg/repo but in checkout you using myorg/repo thats qorking fine for cloning repo but not for push notifications. 

I am facing same problem . Here is my observations 

1. Git hub is delivering the payloads 

=========================================================================

Request URL:

http://jenkins:8080/github-webhook/

Request method:

POST

content-type:

application/json

Expect:

User-Agent:

GitHub-Hookshot/632ecda

X-GitHub-Delivery:

24ec185c-6a48-11e9-87d5-45299c7467cb

X-GitHub-Enterprise-Host:

github.houston.softwaregrp.net

X-GitHub-Enterprise-Version:

2.16.1

X-GitHub-Event:

push

===========================================================================

2. I can see that jenkins  got poked here  http://jenkins:8080/log/all

here is the logs 

 
Apr 28, 2019 11:29:30 PM INFO org.jenkinsci.plugins.github.webhook.subscriber.DefaultPushGHEventSubscriber$1 run
Poked xxxxx-yyyyyy-zzzzzzz-CI
Apr 28, 2019 11:30:00 PM WARNING hudson.triggers.Trigger checkTriggers
 

3. But git hub log is getting updated in below . Its displaying some old log .

http://jenkins:8080/job/jenkins_job/GitHubPollLog/

Same here.

• Webhook configured in GitHub.
• Pipeline configured (GitHub hook trigger for GITScm polling)
• System logs of Jenkins showing each of the webhooks.
• Custom logs mentionned in wiki showing nothing.
• Last GitHub Push page of project showing nothing (Polling has not run yet).

+1

same here

only happens with pipeline job

workaround:   Create a freestyle project like "Trigger pipeline job"  that will call the pipeline job  (trigger other projects..) .