MySQL Remote Connection Problem After A Heavy Usage

I have 2 identical Fedora8 boxes with Apache 2.2.8, MySQL 5.0.45 and PhP 5.2.4. I use one as the Web+DB server (say box A), and the other (box B) just as the Web server connecting to the DB server on box A. I use this 2 machine configuration to test a LAMP based-Web application. I have a client program on other machines that can emulate a massive web workload to these 2 servers; it can emulate hundreds to thousands of users using the application simultaneously.

Before running the test, the connection to the DB server from both boxes seem fine. Using the mysql client program on either box A or B trying to connect to the DB, the connection goes through instantly. In the /etc/my.cnf file, I have max_connections=4096 and max_user_connections=4096. Note that the web app uses one single db user to connect to the db. To allow remote connection, I inserted one record into the user table of the mysql db whose the host field's value is '%' (allow connection from all remote hosts).

After running the test (which I found out that many requests sent to box B failed), mysql client program on box A is still able to connect to the db instantly; but the one on box B has a problem: it takes extremely long (5 - 10 minutes or even more) to establish the connection, it doesn't time out, just takes that long. I believe that's the cause for the failure of requests to box B.