One problem I see is this:
// run the same query as initially was run. no specifiers to db2, should take the default connection
There is no "default connection" in a script; as per the manual for [man]mysql_query/man:
If the link identifier is not specified, the last link opened by mysql_connect() is assumed.
So, I hate to tell you this, but it sounds like you'll have to go through and fix up all of the old code so that it specifically references which link connection is to be used.
This is one (good) reason why PHP/MySQL programmers are suggested to use newer libraries such as MySQLi or PDO, both of which require the link parameter (it's no longer optional, as in the deprecated mysql library).
EDIT: Hrm, just saw this:
mysql_close( $db2 ); // *** triggers the error: Warning: mysql_close(): supplied argument is not a valid MySQL-Link resource in scriptname.php
That's... interesting; I wouldn't have expected that based on your test script.
Can you do a [man]var_dump/man on $db2? What does PHP say about it? Do you have error_reporting set to E_ALL?