Hi,
Congrads!! You actually found what causes the problem, It is
constant value, but you couldn't find where it is... it is normal because you were looking at our VM Template's files, but actually it comes with your Ice VM Cart module. Open that module's PHP file;
/modules/mod_ice_virtuemart_cart/mod_ice_virtuemart_cart.php
and look around 30th - 40th lines, and find this:
$document->addCustomTag('<style type="text/css"> #facebox { top: '.$margin_top.'px!important } </style>');
Delete this line completely and You will be good to go. Your Ice VM Cart will keep working perfectly, honestly; i don't understand why Ice Cart developers have put that constant value there. Weird!
Cheers.