The big difference I can see is where the quantity is changed.
You have...
<font class="ProductPriceConverting">{include file="currency.tpl" value=$price}{if $products[product].ship_price} ({include file="currency.tpl" value=$products[product].ship_price}){/if} x {if $active_modules.Egoods and $products[product].distribution}1<input type="hidden"{else}<input type="text" size="3"{/if} name="productindexes[{$products[product].cartid}]" value="{$products[product].amount}" /> = </font><font class="ProductPrice">{math equation="price*amount" price=$price amount=$products[product].amount format="%.2f" assign=unformatted}{include file="currency.tpl" value=$unformatted}{if $products[product].ship_total} ({include file="currency.tpl" value=$products[product].ship_total}){/if}</font><font class="MarketPrice"> {include file="customer/main/alter_currency_value.tpl" alter_currency_value=$unformatted}{if $products[product].ship_total} {include file="customer/main/alter_currency_value.tpl" alter_currency_value=$products[product].ship_total}{/if}</font>
when the stock cart.tpl has
<font class="ProductPriceConverting">{include file="currency.tpl" value=$price} x {if $active_modules.Egoods and $products[product].distribution}1<input type="hidden"{else}<input type="text" size="3"{/if} name="productindexes[{$products[product].cartid}]" value="{$products[product].amount}" /> = </font><font class="ProductPrice">{math equation="price*amount" price=$price amount=$products[product].amount format="%.2f" assign=unformatted}{include file="currency.tpl" value=$unformatted}</font><font class="MarketPrice"> {include file="customer/main/alter_currency_value.tpl" alter_currency_value=$unformatted}</font>
I have no idea what all of the added code does, but I think that is where the problem lies.
PS - you also have a link to (
http://www.tqualizer.biz) in your cart if it is empty. Do you really want this?