Since 3 or 4 jenkins release (I use 1.653 today), I meet a little problem while jenkins is restarting after plugins upgrade.
Jenkins stays on the main update web page forever.
When I look at the log, I found the following message:

Avertissement: Failed to restart Jenkins
java.lang.RuntimeException: Unexpected issues encountered during cleanUp: null
at jenkins.model.Jenkins.cleanUp(Jenkins.java:2906)
at hudson.lifecycle.UnixLifecycle.restart(UnixLifecycle.java:70)
at jenkins.model.Jenkins$27.run(Jenkins.java:3847)
Caused by: java.lang.UnsupportedOperationException
at java.util.concurrent.CopyOnWriteArrayList$COWIterator.remove(CopyOnWriteArrayList.java:1040)
at hudson.util.PluginServletFilter.cleanUp(PluginServletFilter.java:162)
at jenkins.model.Jenkins._cleanUpPluginServletFilters(Jenkins.java:3238)
at jenkins.model.Jenkins.cleanUp(Jenkins.java:2891)
... 2 more