<grin>.... there's a good reason why you can't find my.cfg, the file is actually called my.cnf🙂 It usually exists in /etc/my.cnf, though it may be in a different spot depending on your installation/distribution.
As for the max connection time, that usually only affects persistent connections (which you're not using) but I s'pose it could also work on orphaned connections opened using mysql_connect(). In theory, PHP should be killing all MySQL connections at the end of the script's execution whether you call mysql_close() or not..... so I'm not really sure why you're being left with all these open processes.
When you use mysql_connect(), are you calling a new connection for every query in your script? Are you calling it once at the outset and then reusing that open connection for all queries? If no resource id is specified for mysql_close(), I believe it will only close the last connection opened. If you call mysql_connect() for every operation, besides being very inefficient, it may be why you're left with all these open processes.
Try doing this, it may help:
$conn = mysql_connect("host", "user", "pass");
// code to select db, query db, and format/display results
mysql_close($conn);
You can also pass $conn into the mysql_select_db() and mysql_query() functions to ensure that the correct connection id is being using, but that's prolly not going to have any affect on your current problem. Left me know how it goes.
-geoff
