Hey Tom,
Sorry you ran into this issues... There hasn't been any logic changes around the port number with the last release that I recall. I'm not sure why you would have that error. 3306 is just the official default port number number used by mysql and what it will try and use if its not present. You can easily specify any port by appending ":portnumber" to the end of the host name field in the installer such as:
localhost:3307
If you want to force the port number in code just open up the installer.php file and comment out these two lines (around line number 158)
//$_POST['dbport'] = isset($_POST['dbhost']) ? parse_url($_POST['dbhost'], PHP_URL_PORT) : 3306;
//$_POST['dbport'] = (! empty($_POST['dbport'])) ? $_POST['dbport'] : 3306;
$_POST['dbport'] = 3307; //Some other port
and then set the port number directly.
If you need help looking deeper into the issue feel free to submit a support ticket and then just reference this thread, I can take a look and see what may have happened that still allows for the older installer file to work...
Thanks~