I had the same problem
I am sure you have only once the code, which only track the URL, if outgoinglink are activated Iguess.
but it sorted after this and it adds up every time you click on the link.
Code:
<div class="top">
<div class="toptitle" id="ls_thetitle-{$link_shakebox_index}">
{if $use_title_as_link eq true}
{if $url_short neq "http://" && $url_short neq "://" && $url_short neq "1"} <a onclick="sendClickedValue({$link_id},{$link_shakebox_index});" href="{$url}" {if $open_in_new_window eq true} target="_blank"{/if}>{$title_short}</a>
{else}
<a href="{$story_url}" onclick="sendClickedValue({$link_id},{$link_shakebox_index});">{$title_short}</a>
{/if}
{else}
{if $pagename eq "story"}
{if $url_short eq "http://" OR $url_short eq "://" OR $url_short eq "1"}
{$title_short}
{else}
<a href="{$story_url}" onclick="sendClickedValue({$link_id},{$link_shakebox_index});">{$title_short}</a>
{/if}
{else}
<a href="{$story_url}" onclick="sendClickedValue({$link_id},{$link_shakebox_index});">{$title_short}</a>
{/if}
{/if}
</div>