[kube]

The original search box is located further down in head.tpl using the same code as I mentioned.

Also where you have placed the new snip into the TD HeadRightBox, surround it with {if $main ne "fast_lane_checkout"} so it looks like...

<td class="HeadRightBox">
{if $main ne "fast_lane_checkout"}
{if $usertype eq "C"}
{ include file="customer/search.tpl" }
{/if}
{/if}
</td>