By template tag I mean the slideshow template tag, the function that is used to add the slideshow to a template file. This is how the tag currently looks in your header.php file:
<?php if ( function_exists( 'meteor_slideshow' ) ) { meteor_slideshow(); } ?>There is no slideshow specified, so it is loading all the latest slides. When you are using multiple slideshows, create each slideshow in the admin and specify it so that only those slides are loaded.
Like, you could create a "header" slideshow, add the header slides to it, and then load that in the header instead:
<?php if ( function_exists( 'meteor_slideshow' ) ) { meteor_slideshow( "header", "" ); } ?>