I've seen this a few times in the past:

Exception in thread "Ping thread for channel hudson.remoting.Channel@63b204d9:channel" java.lang.NullPointerException
at jenkins.slaves.PingFailureAnalyzer.all(PingFailureAnalyzer.java:31)
at hudson.slaves.ChannelPinger$1.onDead(ChannelPinger.java:111)
at hudson.remoting.PingThread.ping(PingThread.java:126)
at hudson.remoting.PingThread.run(PingThread.java:85)
Mar 29, 2016 12:05:10 PM hudson.remoting.SynchronousCommandTransport$ReaderThread run
SEVERE: I/O error in channel channel
java.net.SocketTimeoutException: Read timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.socketRead(Unknown Source)
at java.net.SocketInputStream.read(Unknown Source)
at java.net.SocketInputStream.read(Unknown Source)
at java.io.BufferedInputStream.fill(Unknown Source)
at java.io.BufferedInputStream.read(Unknown Source)
at hudson.remoting.FlightRecorderInputStream.read(FlightRecorderInputStream.java:82)
at hudson.remoting.ChunkedInputStream.readHeader(ChunkedInputStream.java:72)
at hudson.remoting.ChunkedInputStream.readUntilBreak(ChunkedInputStream.java:103)
at hudson.remoting.ChunkedCommandTransport.readBlock(ChunkedCommandTransport.java:39)
at hudson.remoting.AbstractSynchronousByteArrayCommandTransport.read(AbstractSynchronousByteArrayCommandTransport.java:34)
at hudson.remoting.SynchronousCommandTransport$ReaderThread.run(SynchronousCommandTransport.java:48)

Though I haven't looked at it in a while, IIRC,\ Jenkins.getInstance() was failing and returning null.