Well I would like to know how the login does not work on our screen. It should but you can gladly change the links on the menubar by editing pp-inc.php and changing the links for login by editing the function topmenu
if ( VB3_INTEGRATION == "off" ) $log = "· <a href=\"{$Globals['maindir']}/misc.php?action=login&login=yes\">{$Globals['pp_lang']['login']}</a>";
to say
if ( VB3_INTEGRATION == "off" ) $log = "· <a href=\"{$Globals['vbulletin']}//index.php?action=login\">{$Globals['pp_lang']['login']}</a>";
In the smf.php file in the forums directory I show the register link as this which would appear correct
$regtext = " · <a href=\"{$Globals['vbulletin']}/register.php?1\">{$Globals['pp_lang']['register']}</a>";