Spot on my friend, thank you very much.
I put my get_header() back into single.php, and added in this line of code to remove the header/navigation from the single page only:
header.php:
<?php if( !is_single() ) { ?>
<div id="header">
</div><!-- header -->
<div id="navigation">
</div><!-- navigation -->
<?php } ?>
This means the header and navigation will only show when the page is not single.php
I have other pages on my site (other than the homepage) which require the header and navigation menu and all my single posts are launched into a new child window which does not require the header/navigation.
Thanks again for the speedy reply,
Smithy.