Is there any reason why the $owner_id wouldn't be available when calling a Payment script? I can get $site_id just fine.

$conDat = array('_SiteId1' => $site_id, //passes the site id into IS
'_OwnerId' => $owner_id,
'_PaymentRef' => $payment_ref); //passes the Owner id into IS

$owner_id is always blank. If I assign it before the array it populates just fine so I know it isn't a problem with the array.

Any help would be appreciated.

The owner ID is computed by the front-end and is the standard current Joomla user ID

$user =& JFactory::getUser();
$owner_id = $user->id;

It corresponds to the current logged user and is used when creating the slave site.