Did you make any progress with this? We are experiencing the same kind of errors, on occasion, even when a new connection is created, on RHEL ES release 4 (update 4) with mysql 5 and connector 3.1.13. e.g. stack trace
java.io.EOFException
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:798)
at com.mysql.jdbc.MysqlIO.secureAuth411(MysqlIO.java:3700)
at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1203)
at com.mysql.jdbc.Connection.createNewIO(Connection.java:2568)
at com.mysql.jdbc.Connection.<init>(Connection.java:1485)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:266)
at java.sql.DriverManager.getConnection(DriverManager.java:525)
at java.sql.DriverManager.getConnection(DriverManager.java:171)
