help: Mysql locking tables and persistent connections..

I am trying to avoid some concurrency problems by using locking tables in mysql. Problem is, I already locked the tables and still had a concurrency problem. Our first guess is that since we are accesing the table with the same user, then when it ignores the log since it is the same user. But this cant be the way it works. I imagine its per process, not per user. But then, we are using persistent connections. Does this influence table locking ?? any ideas or thoughts on this are greatly appreciated... I know I am missing something here.