Sounds like this isn't reproducible, so closing. Re-open if you can give reproduction steps. Thanks!

Figured out my issue – i had a varnish cache running in front of Jenkins, which was apparently caching something bad that was breaking the UI after i changed the version of the pipeline plugin. And causing the pipeline entry box not to display.

This tells me that Jenkins might not sending the proper cache-control headers for one of the configuration page responses.

Also noticed this error in the job configuration console:

"NetworkError: 404 Not Found - http://<site>/jenkins/$stapler/bound/5c424e6d-b6c6-4fa1-a20b-99c0516b8539/render"
"NetworkError: 404 Not Found - http://<site>/jenkins/$stapler/bound/0e1fffc7-0411-4784-bdea-de3e634962a1/render"

The error on submit could possibly just be related to the failure of the GUI to draw the boxes with which to input the pipeline script.

Here's the crash in text form so it can be searched easier:

Jun 10, 2016 5:09:39 PM org.apache.catalina.core.ApplicationContext log
SEVERE: Error while serving http://.../jenkins/job/t4stestete/configSubmit
java.lang.reflect.InvocationTargetException
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$InstanceFunction.invoke(Function.java:324)
at org.kohsuke.stapler.interceptor.RequirePOST$Processor.invoke(RequirePOST.java:52)
at org.kohsuke.stapler.PreInvokeInterceptedFunction.invoke(PreInvokeInterceptedFunction.java:26)
at org.kohsuke.stapler.Function.bindAndInvoke(Function.java:167)
at org.kohsuke.stapler.Function.bindAndInvokeAndServeResponse(Function.java:100)
at org.kohsuke.stapler.MetaClass$1.doDispatch(MetaClass.java:124)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:58)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:746)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:876)
at org.kohsuke.stapler.MetaClass$5.doDispatch(MetaClass.java:233)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:58)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:746)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:876)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:649)
at org.kohsuke.stapler.Stapler.service(Stapler.java:238)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:604)
at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:543)
at org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:461)
at org.apache.catalina.core.StandardHostValve.throwable(StandardHostValve.java:412)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:201)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:683)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NullPointerException
at org.jenkinsci.plugins.scriptsecurity.scripts.ScriptApproval.hash(ScriptApproval.java:364)
at org.jenkinsci.plugins.scriptsecurity.scripts.ScriptApproval.configuring(ScriptApproval.java:416)
at org.jenkinsci.plugins.workflow.cps.CpsFlowDefinition.<init>(CpsFlowDefinition.java:70)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.kohsuke.stapler.RequestImpl.invokeConstructor(RequestImpl.java:525)
at org.kohsuke.stapler.RequestImpl.instantiate(RequestImpl.java:777)
at org.kohsuke.stapler.RequestImpl.access$200(RequestImpl.java:83)
at org.kohsuke.stapler.RequestImpl$TypePair.convertJSON(RequestImpl.java:674)
at org.kohsuke.stapler.RequestImpl.bindJSON(RequestImpl.java:478)
at org.kohsuke.stapler.RequestImpl.bindJSON(RequestImpl.java:474)
at org.jenkinsci.plugins.workflow.job.WorkflowJob.submit(WorkflowJob.java:174)
at hudson.model.Job.doConfigSubmit(Job.java:1229)
... 40 more

I have this problem with 2.6+2.8. I even tried wiping ALL plugins and reinstalling my set of plugins from scratch using the update center. I also wiped the tomcat work and temp directories. Same error. There are no plugin load errors in the catalina.out.

If you installed plugins manually, very likely you missed some mandatory dependencies. Currently Jenkins core does not do a good job of reporting these properly. A fix for that is in progress. What the actual NPE here is, I am not sure offhand.