We reported an issue some time back that was also listed as fixed in Jenkins 1.441:
Log:
[FIXED JENKINS-11130] SEVERE: I/O error in channel Chunked connection when using jenkins-cli.jar

Perhaps another bug should NOT be submitted so I have added the following comments below the line to the original defect 11130 comments section in case it can be reviewed/re-opened.

We did NOT try to make any adjustments to the Tomcat configuration:

Tomcat Connector connectionUploadTimeout

but we are also now seeing the same problem with Winstone when at this same 1.441 level. We did revert to the 1.438 version of the CLI (leaving the WAR at 1.441 running in Winstone) and that is serving asthe current workaround.

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We have downloaded and installed the LATEST 1.441 release that lists the fix for this problem. Currently we were running 1.438 on Winstone only (since with Tomcat 6 or 7, we had experienced the error HOWEVER yet under Winstone, it worked OK so that was our workaround - while running 1.438).

Now with Jenkins 1.441 - we are getting the ERROR again and NOW WITH BOTH Winstone and the Tomcat configurations). We have left the Jenkins 1.441 WAR file in place running on Winstone, and reverted the CLI jar file back to the 1.438 version for now and that appears to work again with Winstone.

Checked Manifest of CLI jar downloaded with the 1.441 WAR installation:

Manifest-Version: 1.0
Archiver-Version: Plexus Archiver
Created-By: Apache Maven
Built-By: kohsuke
Build-Jdk: 1.6.0_26
Main-Class: hudson.cli.CLI
Jenkins-CLI-Version: 1.441

Under Tomcat 7, we get this stacktrace:

Started by command line
[workspace] $ /bin/bash -xe /opt/apache-tomcat-7.0.22_jenkins/temp/hudson32817888834817830.sh
+ /opt/Sun/jdk1.6.0_14/bin/java -jar /opt/Sun/jdk1.6.0_14/lib/jenkins-cli.jar -s http://11.22.33.44:8082/jenkins/ build XYZ_Project-SharedLibs -s -p SVN_PATH=trunk
Dec 5, 2011 12:59:11 PM hudson.remoting.Channel$ReaderThread run
SEVERE: I/O error in channel Chunked connection to http://11.22.33.44:8082/jenkins/cli
java.io.IOException: Unexpected termination of the channel
at hudson.remoting.Channel$ReaderThread.run(Channel.java:1115)
Caused by: java.io.EOFException
at java.io.ObjectInputStream$BlockDataInputStream.peekByte(ObjectInputStream.java:2554)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1297)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:351)
at hudson.remoting.Channel$ReaderThread.run(Channel.java:1109)
Exception in thread "main" hudson.remoting.RequestAbortedException: hudson.remoting.RequestAbortedException: java.io.IOException: Unexpected termination of the channel
at hudson.remoting.Request.call(Request.java:149)
at hudson.remoting.Channel.call(Channel.java:681)
at hudson.remoting.RemoteInvocationHandler.invoke(RemoteInvocationHandler.java:158)
at $Proxy2.main(Unknown Source)
at hudson.cli.CLI.execute(CLI.java:200)
at hudson.cli.CLI._main(CLI.java:330)
at hudson.cli.CLI.main(CLI.java:245)
Caused by: hudson.remoting.RequestAbortedException: java.io.IOException: Unexpected termination of the channel
at hudson.remoting.Request.abort(Request.java:273)
at hudson.remoting.Channel.terminate(Channel.java:732)
at hudson.remoting.Channel$ReaderThread.run(Channel.java:1139)
Caused by: java.io.IOException: Unexpected termination of the channel
at hudson.remoting.Channel$ReaderThread.run(Channel.java:1115)
Caused by: java.io.EOFException
at java.io.ObjectInputStream$BlockDataInputStream.peekByte(ObjectInputStream.java:2554)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1297)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:351)
at hudson.remoting.Channel$ReaderThread.run(Channel.java:1109)
Build step 'Execute shell' marked build as failure
Notifying upstream projects of job completion
Finished: FAILURE

Under Winstone, we get this stacktrace - it's somewhat different:

Started by command line
[workspace] $ /bin/bash -xe /tmp/hudson10791816374444704.sh
+ /opt/Sun/jdk1.6.0_14/bin/java -jar /opt/Sun/jdk1.6.0_14/lib/jenkins-cli.jar -s http://11.22.33.44:8082/jenkins/ build XYZ_Project-SharedLibs -s -p SVN_PATH=trunk
Dec 5, 2011 1:18:22 PM hudson.remoting.Channel$ReaderThread run
SEVERE: I/O error in channel Chunked connection to http://11.22.33.44:8082/jenkins/cli
java.io.IOException: Premature EOF
at sun.net.www.http.ChunkedInputStream.readAheadBlocking(ChunkedInputStream.java:538) (http://www.http.ChunkedInputStream.readAheadBlocking%28ChunkedInputStream.java:538%29)
at sun.net.www.http.ChunkedInputStream.readAhead(ChunkedInputStream.java:582) (http://www.http.ChunkedInputStream.readAhead%28ChunkedInputStream.java:582%29)
at sun.net.www.http.ChunkedInputStream.read(ChunkedInputStream.java:669) (http://www.http.ChunkedInputStream.read%28ChunkedInputStream.java:669%29)
at java.io.FilterInputStream.read(FilterInputStream.java:116)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2504) (http://www.protocol.http.HttpURLConnection$HttpInputStream.read%28HttpURLConnection.java:2504%29)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2499) (http://www.protocol.http.HttpURLConnection$HttpInputStream.read%28HttpURLConnection.java:2499%29)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2488) (http://www.protocol.http.HttpURLConnection$HttpInputStream.read%28HttpURLConnection.java:2488%29)
at java.io.ObjectInputStream$PeekInputStream.peek(ObjectInputStream.java:2249)
at java.io.ObjectInputStream$BlockDataInputStream.peek(ObjectInputStream.java:2542)
at java.io.ObjectInputStream$BlockDataInputStream.peekByte(ObjectInputStream.java:2552)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1297)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:351)
at hudson.remoting.Channel$ReaderThread.run(Channel.java:1109)
Exception in thread "main" hudson.remoting.RequestAbortedException: hudson.remoting.RequestAbortedException: java.io.IOException: Premature EOF
at hudson.remoting.Request.call(Request.java:149)
at hudson.remoting.Channel.call(Channel.java:681)
at hudson.remoting.RemoteInvocationHandler.invoke(RemoteInvocationHandler.java:158)
at $Proxy2.main(Unknown Source)
at hudson.cli.CLI.execute(CLI.java:200)
at hudson.cli.CLI._main(CLI.java:330)
at hudson.cli.CLI.main(CLI.java:245)
Caused by: hudson.remoting.RequestAbortedException: java.io.IOException: Premature EOF
at hudson.remoting.Request.abort(Request.java:273)
at hudson.remoting.Channel.terminate(Channel.java:732)
at hudson.remoting.Channel$ReaderThread.run(Channel.java:1139)
Caused by: java.io.IOException: Premature EOF
at sun.net.www.http.ChunkedInputStream.readAheadBlocking(ChunkedInputStream.java:538) (http://www.http.ChunkedInputStream.readAheadBlocking%28ChunkedInputStream.java:538%29)
at sun.net.www.http.ChunkedInputStream.readAhead(ChunkedInputStream.java:582) (http://www.http.ChunkedInputStream.readAhead%28ChunkedInputStream.java:582%29)
at sun.net.www.http.ChunkedInputStream.read(ChunkedInputStream.java:669) (http://www.http.ChunkedInputStream.read%28ChunkedInputStream.java:669%29)
at java.io.FilterInputStream.read(FilterInputStream.java:116)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2504) (http://www.protocol.http.HttpURLConnection$HttpInputStream.read%28HttpURLConnection.java:2504%29)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2499) (http://www.protocol.http.HttpURLConnection$HttpInputStream.read%28HttpURLConnection.java:2499%29)
at sun.net.www.protocol.http.HttpURLConnection$HttpInputStream.read(HttpURLConnection.java:2488) (http://www.protocol.http.HttpURLConnection$HttpInputStream.read%28HttpURLConnection.java:2488%29)
at java.io.ObjectInputStream$PeekInputStream.peek(ObjectInputStream.java:2249)
at java.io.ObjectInputStream$BlockDataInputStream.peek(ObjectInputStream.java:2542)
at java.io.ObjectInputStream$BlockDataInputStream.peekByte(ObjectInputStream.java:2552)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1297)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:351)
at hudson.remoting.Channel$ReaderThread.run(Channel.java:1109)
Build step 'Execute shell' marked build as failure
Notifying upstream projects of job completion
Finished: FAILURE