Jenkins version 1.568,after update to 1.569,issue still remains.
It's a little bit complicated to reproduce the bug. The Jenkins server we use is behind the firewall with limited access to the internet.So one day our ops decide to update the plugin we use on a whim,when he re-login to check the status later,all plugin just vanished.Not just disappear from the plugin manager list,the plugin files don't exist on the system too.

And here's some log:

Jun 26, 2014 4:58:17 PM jenkins.InitReactorRunner$1 onTaskFailed
SEVERE: Failed Inspecting plugin /data/jenkins/plugins/cvs.jpi
java.io.IOException: Failed to expand /data/jenkins/plugins/cvs.jpi
at hudson.ClassicPluginStrategy.explode(ClassicPluginStrategy.java:484)
at hudson.ClassicPluginStrategy.createPluginWrapper(ClassicPluginStrategy.java:150)
at hudson.PluginManager$1$3$1.run(PluginManager.java:240)
at org.jvnet.hudson.reactor.TaskGraphBuilder$TaskImpl.run(TaskGraphBuilder.java:169)
at org.jvnet.hudson.reactor.Reactor.runTask(Reactor.java:282)
at jenkins.model.Jenkins$7.runTask(Jenkins.java:885)
at org.jvnet.hudson.reactor.Reactor$2.run(Reactor.java:210)
at org.jvnet.hudson.reactor.Reactor$Node.run(Reactor.java:117)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)
Caused by: Error while expanding /data/jenkins/plugins/cvs.jpi
java.util.zip.ZipException: archive is not a ZIP archive
at org.apache.tools.ant.taskdefs.Expand.expandFile(Expand.java:192)
at org.apache.tools.ant.taskdefs.Expand.execute(Expand.java:132)
at hudson.ClassicPluginStrategy.unzipExceptClasses(ClassicPluginStrategy.java:556)
at hudson.ClassicPluginStrategy.explode(ClassicPluginStrategy.java:481)
... 10 more
Caused by: java.util.zip.ZipException: archive is not a ZIP archive
at org.apache.tools.zip.ZipFile.positionAtCentralDirectory(ZipFile.java:481)
at org.apache.tools.zip.ZipFile.populateFromCentralDirectory(ZipFile.java:320)
at org.apache.tools.zip.ZipFile.<init>(ZipFile.java:186)
at org.apache.tools.ant.taskdefs.Expand.expandFile(Expand.java:170)
... 13 more