I had exactly the same issue.However, i have narrowed this functionality working for us in 1.554_3 ( http://mirrors.jenkins-ci.org/war-stable/1.554.3/) and newer version is failing.
We use LDAP for security. All the users are validated by AD, and the roles are retrieved from LDAP. We can login with LDAP user/pass successfully. If i have a keyfile attached to the AD user, the CLI functionality works fine too.
However, we also have a user called "AutoJobBuilder" which does not exists in LDAP, and i have entered that as user in the jenkins [ Configure Global Security -> Authorization -> Project-based Matrix Authorization Strategy ]
[ Security Realm -> LDAP ]
Last week we upgraded jenkins to latest version, and we started facing this issue. As i started my investigation i find that till version 1.554_3 it works fine, and then it stops working.
As i understand, the issue seems to be a change in functionality. pre 1.554_3, the "static" user is not checked in AD. but post 1.554_3, its checked in AD for existence, but does not exists and it fails.
Exception in thread "main" java.io.EOFException
SERVER ERROR LOG:
06-Oct-2014 10:08:50 hudson.TcpSlaveAgentListener$ConnectionHandler run
INFO: Accepted connection #1 from /126.96.36.199:34528
Exception in thread "Thread-346" org.acegisecurity.userdetails.UsernameNotFoundException: User AutoJobBuilder not found in directory.
06-Oct-2014 10:08:52 hudson.model.Run execute