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Breadcrumb separator does not have a wrapper to differentiate of the other components of the breadcrumb. The solution for this issue is to use this instruction in template.php in breadcrumb section:
$separator = theme('html_tag', array(
'element' => array(
'#tag' => 'span',
'#attributes' => array(
'class' => 'breadcrumb-separator',
),
'#value' => filter_xss(theme_get_setting('breadcrumb_separator')),
),
));