I'm using github-plugin v1.20.0 but not github-sqs and having the same issue when saving config. After downgrading back to v1.9.1 everything seem to be fine.

https://github.com/jenkinsci/github-plugin/commit/a1f53cdb15bcddc0e719ec6eacf03d3fe6ea5e07

{{
javax.servlet.ServletException: java.lang.NullPointerException
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:796)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:876)
at org.kohsuke.stapler.MetaClass$6.doDispatch(MetaClass.java:249)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:53)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:746)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:876)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:649)
at org.kohsuke.stapler.Stapler.service(Stapler.java:238)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:686)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1494)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:132)
at hudson.plugins.audit_trail.AuditTrailFilter.doFilter(AuditTrailFilter.java:95)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:129)
at hudson.plugins.greenballs.GreenBallFilter.doFilter(GreenBallFilter.java:58)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:129)
at hudson.util.PluginServletFilter.doFilter(PluginServletFilter.java:123)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1482)
at hudson.security.csrf.CrumbFilter.doFilter(CrumbFilter.java:49)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1482)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:84)
at hudson.security.UnwrapSecurityExceptionFilter.doFilter(UnwrapSecurityExceptionFilter.java:51)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at jenkins.security.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:117)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.providers.anonymous.AnonymousProcessingFilter.doFilter(AnonymousProcessingFilter.java:125)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.ui.rememberme.RememberMeProcessingFilter.doFilter(RememberMeProcessingFilter.java:142)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:271)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at jenkins.security.BasicHeaderProcessor.doFilter(BasicHeaderProcessor.java:93)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:249)
at hudson.security.HttpSessionContextIntegrationFilter2.doFilter(HttpSessionContextIntegrationFilter2.java:67)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at hudson.security.ChainedServletFilter.doFilter(ChainedServletFilter.java:76)
at hudson.security.HudsonFilter.doFilter(HudsonFilter.java:171)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1482)
at org.kohsuke.stapler.compression.CompressionFilter.doFilter(CompressionFilter.java:49)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1482)
at hudson.util.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:81)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1482)
at org.kohsuke.stapler.DiagnosticThreadNameFilter.doFilter(DiagnosticThreadNameFilter.java:30)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1474)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:499)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:533)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:428)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
at org.eclipse.jetty.server.Server.handle(Server.java:370)
at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:489)
at org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:960)
at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:1021)
at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865)
at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:240)
at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:668)
at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:52)
at winstone.BoundedExecutorService$1.run(BoundedExecutorService.java:77)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NullPointerException
at com.cloudbees.jenkins.GitHubRepositoryNameContributor$FromSCM.parseAssociatedNames(GitHubRepositoryNameContributor.java:85)
at com.cloudbees.jenkins.GitHubRepositoryNameContributor.parseAssociatedNames(GitHubRepositoryNameContributor.java:42)
at com.cloudbees.jenkins.Cleaner.onStop(Cleaner.java:43)
at com.cloudbees.jenkins.GitHubPushTrigger.stop(GitHubPushTrigger.java:163)
at hudson.model.AbstractProject.submit(AbstractProject.java:1882)
at hudson.model.Project.submit(Project.java:230)
at hudson.model.Job.doConfigSubmit(Job.java:1206)
at hudson.model.AbstractProject.doConfigSubmit(AbstractProject.java:796)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.kohsuke.stapler.Function$InstanceFunction.invoke(Function.java:298)
at org.kohsuke.stapler.Function.bindAndInvoke(Function.java:161)
at org.kohsuke.stapler.Function.bindAndInvokeAndServeResponse(Function.java:96)
at org.kohsuke.stapler.MetaClass$1.doDispatch(MetaClass.java:121)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:53)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:746)
... 67 more
}}

Cried victory too soon. In my case it happens consistently when creating a new job, not setting the git url (because it's used as a template) and saving the config. It's probably not able to fetch the contributor list on an empty git repo.

In the version 1.9.1 the exception happens at
com.cloudbees.jenkins.GitHubRepositoryNameContributor$FromSCM.parseAssociatedNames(GitHubRepositoryNameContributor.java:59)

It also seem to interfere with the multi-branch-project-plugin plugin. Supposedly because the root project doesn't checkout the code either.

Code changed in jenkins
User: Mark Guzman
Path:
src/main/java/com/base2services/jenkins/SqsBuildTrigger.java
http://jenkins-ci.org/commit/github-sqs-plugin/1a350eef3e47c501d6c0101d4d47e3d3ed70f34d
Log:
adding a null check to try to prevent an NPE. hopefully resolving
JENKINS-24839

Code changed in jenkins
User: Aaron Walker
Path:
src/main/java/com/base2services/jenkins/SqsBuildTrigger.java
http://jenkins-ci.org/commit/github-sqs-plugin/b9a38ce5083e866eca4a34dfd281b18f62069524
Log:
Merge pull request #4 from segfault/master

adding a null check to try to prevent an NPE. hopefully resolving JENKINS-24839

Compare: https://github.com/jenkinsci/github-sqs-plugin/compare/bcd61e823e5d...b9a38ce5083e