LDAP Connection TimeOut Exception

You can send a SIGQUIT signal to the running JVM to get each thread's stacktraces printed to stdout. This doesn't kill the process, though I think it does put all threads to sleep while the stack traces are being printed.

Then, correlate the thread IDs listed with your preferred method of seeing thread-wise CPU utilization. prstat -L for Solaris, top -H for Linux. Note that the tid's in the java stack traces are printed in hexadecimal; you'll probably have to convert to decimal when comparing to top or prstat output.

Please note the --skip-networking parameter

Yes, very likely the cause of the issue. Remove skip-networking and add "bind-address=127.0.0.1" instead in my.cnf.

I guess java connects via network only and does not use socket connections, which is what you do with mysql cli tools.