For example, you are opening two separate connections to two different databases (but on the same host, and with the same user and password):

$db1 = mysql_connect($dbhost, $dbuser, $dbpass);
$rv = mysql_select_db($dbname1, $db1);
$db2 = mysql_connect($dbhost, $dbuser, $dbpass);
$rv = mysql_select_db($dbname2, $db2);

At this point, both $db1 and $db2 will have selected the database named by $dbname2.

The workaround is to require that the second MySQL connection is new:

$db1 = mysql_connect($dbhost, $dbuser, $dbpass);
$rv = mysql_select_db($dbname1, $db1);
$db2 = mysql_connect($dbhost, $dbuser, $dbpass, TRUE);
$rv = mysql_select_db($dbname2, $db2);

Now, $db1 should have selected $dbname1, and $db2 should have selected $dbname2.