My guess is you created two separate new areas instead of creating one area with two widget area's in it (confusing I know)
I'm going to guess you setup your header area like this:
HTML Code:
%bar1 <?php bfa_widget_area('name=headerlogo&cells=1&before_widget=<div id="%1$s" class="header-widget %2$s">&after_widget=</div>'); ?> <?php bfa_widget_area('name=headerslideshow&cells=1&before_widget=<div id="%1$s" class="header-widget %2$s">&after_widget=</div>'); ?>
when you could have done this
HTML Code:
%bar1 <?php bfa_widget_area('name=header_widgets&cells=2&before_widget=<div id="%1$s" class="header-widget %2$s">&after_widget=</div>'); ?>
This would give you two widget areas in the same Header_Widget area (wrapped in a <div>...</div>) so they will line up.
If you want to change it, first remove the widgets from the current widget areas, then delete the widget areas, then add the new widget area, then add the widgets back in.
This is to make sure you don't leave orphaned info in the database.