Where in the atlassian-user.xml file do you specify a password? At least I think that's my missing link based on the log file below.
[2012-09-28 10:44:22,776] INFO ###########################################################################################################################
[2012-09-28 10:44:22,776] INFO
[2012-09-28 10:44:22,776] INFO LDAP Support Tool version 2.0
[2012-09-28 10:44:22,776] INFO
[2012-09-28 10:44:22,776] INFO ###########################################################################################################################
[2012-09-28 10:44:22,980] ERROR Failed to connect to LDAP server: Username or password is incorrect. Please check them again.
com.atlassian.paddle.connection.ConnectionException: Username or password is incorrect. Please check them again.
at com.atlassian.paddle.connection.DefaultConnectionFactory.createFriendlyLdapException(DefaultConnectionFactory.java:43)
at com.atlassian.paddle.connection.DefaultConnectionFactory.createConnection(DefaultConnectionFactory.java:34)
at com.atlassian.paddle.task.DefaultTaskRunner.runTask(DefaultTaskRunner.java:33)
at com.atlassian.paddle.Paddle.main(Paddle.java:64)
Caused by: javax.naming.AuthenticationException: [LDAP: error code 49 - 80090308: LdapErr: DSID-0C090334, comment: AcceptSecurityContext error, data 525, vece ]
at com.sun.jndi.ldap.LdapCtx.mapErrorCode(LdapCtx.java:3067)
at com.sun.jndi.ldap.LdapCtx.processReturnCode(LdapCtx.java:3013)
at com.sun.jndi.ldap.LdapCtx.processReturnCode(LdapCtx.java:2815)
at com.sun.jndi.ldap.LdapCtx.connect(LdapCtx.java:2729)
at com.sun.jndi.ldap.LdapCtx.<init>(LdapCtx.java:296)
at com.sun.jndi.ldap.LdapCtxFactory.getUsingURL(LdapCtxFactory.java:175)
at com.sun.jndi.ldap.LdapCtxFactory.getUsingURLs(LdapCtxFactory.java:193)
at com.sun.jndi.ldap.LdapCtxFactory.getLdapCtxInstance(LdapCtxFactory.java:136)
at com.sun.jndi.ldap.LdapCtxFactory.getInitialContext(LdapCtxFactory.java:66)
at javax.naming.spi.NamingManager.getInitialContext(NamingManager.java:667)
at javax.naming.InitialContext.getDefaultInitCtx(InitialContext.java:288)
at javax.naming.InitialContext.init(InitialContext.java:223)
at javax.naming.InitialContext.<init>(InitialContext.java:197)
at javax.naming.directory.InitialDirContext.<init>(InitialDirContext.java:82)
at com.atlassian.paddle.connection.DefaultConnectionFactory.createConnection(DefaultConnectionFactory.java:27)
... 2 more
