It seems like you have some bug in your style. If default is working fine it means that vBET is working fine.
Please note that when you chose NAVBAR-TOP then vBET adds flags using plugin named Add flags and this part of code:
PHP Code:
} else if ('nt' == $vbulletin->options['vbenterprisetranslator_flagsplace']) {
vB_Template::preRegister('navbar', array('vbenterprisetranslatorflags' => $vbenterprisetranslatorflags));
$vbulletin->templatecache['navbar'] = substr_replace($vbulletin->templatecache['navbar'], ' $vbenterprisetranslatorflags .', 17,1);
} else if ...
It is assumed that content of $vbulletin->templatecache['navbar'] starts with '$final_rendered = '.
Do you need more help here?