Let me see if I can explain something.
When you use the theme options (ato->Style WIDGETS->Widget Container) to do some styling, it creates a CSS selector 'div.widget' and puts your rules under that. Then the widgets are created with code like
HTML Code:
<div id="text-6" class="widget widget_text">
and the CSS is applied.
Now when you create a new widget area and add the new widget option
HTML Code:
&before_widget=<div id="%1$s" class="Header-widget %2$s">&after_widget=</div>
you are saying "I want to change the classes that are assigned to my new widget area and give it a class of 'header-widget'". Now the widget code will look like this
HTML Code:
<div id="calendar-9" class="Header-widget widget_calendar">
and since this does not match the selector 'div.widget' the rules from the widget area styling
does not get applied.
Now if you changed the new widget code from
HTML Code:
<?php bfa_widget_area('name=Header widget&cells=3&align=2&width_1=675&width_3=240&before_widget=<div id="%1$s" class="Header-widget %2$s">&after_widget=</div>');?>
to
HTML Code:
<?php bfa_widget_area('name=Header widget&cells=3&align=2&width_1=675&width_3=240&before_widget=<div id="%1$s" class="widget %2$s">&after_widget=</div>');?>
or
HTML Code:
<?php bfa_widget_area('name=Header widget&cells=3&align=2&width_1=675&width_3=240&before_widget=<div id="%1$s" class="Header-widget widget %2$s">&after_widget=</div>');?>
or even
HTML Code:
<?php bfa_widget_area('name=Header widget&cells=3&align=2&width_1=675&width_3=240');?>
the code would be
HTML Code:
<div id="calendar-9" class="widget widget_calendar">
and this code matchs the selector 'div.widget', so the rules from the widget area styling
get applied.
I hope this helps.