This is only happening on our live linux server, and only with version 2.4.4 and 2.4.5.
When $BaseHref is used in a template, the url that is generated is "http://domain.com/index.php". Therefore take the following:
<a href="{$BaseHref}"><img src="{$BaseHref}/themes/challenger/images/Logo.png" alt="Logo Image" /></a>
is output as follows
<a href="http://ats.ecomcorp.co.nz/index.php/"><img src="http://ats.ecomcorp.co.nz/index.php//themes/challenger/images/Logo.png" alt="Logo Image" /></a>
Any Ideas? This is all fine on the Windows/WAMP box.