I am able to mysqlcheck using the same credentials from the command line on the web server, and the config info that it prints when I try to access http://myserver.com/nubuilder/nuinstall.php is all correct.
Here is where is gets confusing: if I go through nuinstall_lib.php and manually replace the $DBvars read from config.php with string literals like this:
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//$con = mysql_connect($DBHost,$DBUserID,$DBPassWord);
$con = mysql_connect("db.myhostnameisreallylong.com","userName","p4ssw0rd!!");
//$sdb = mysql_select_db($DBName,$con);
$sdb = mysql_select_db("myDatabase",$con);
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diveguy@p3nlhftpg017 nuBuilder :) $ mysql --version
mysql Ver 14.12 Distrib 5.0.77, for redhat-linux-gnu (i686) using readline 5.1
diveguy@p3nlhftpg017 nuBuilder :) $ uname -a
Linux p3nlhftpg017.shr.prod.phx3.secureserver.net 2.6.18-402.el5PAE #1 SMP Tue Feb 10 18:29:18 EST 2015 i686 i686 i386 GNU/Linux
diveguy@p3nlhftpg017 nuBuilder :) $ php-config --version
4.4.9
diveguy@p3nlhftpg017 nuBuilder :) $