1 open your style sheet and find

#logoWrapper{
background-image: url(header_bg.jpg);
background-repeat: no-repeat;
background-position: left bottom;
background-color: #ffffff;
height: 94px;
}


change the height to 90px

2 open includes/languages/english/header.php and find this section

define('HEADER_ALT_TEXT', 'Powered by Zen Cart :: The Art of E-Commerce');
define('HEADER_SALES_TEXT', 'TagLine Here');
define('HEADER_LOGO_WIDTH', '192px');
define('HEADER_LOGO_HEIGHT', '64px');
define('HEADER_LOGO_IMAGE', 'logo.gif');

make sure the image height is set to 90px