on the cart display page, change:
<td class="eC_FormItem"><input type="checkbox" value="<?php echo $cupcake1->DisplayInfo("ID"); ?>" name="cupcake1_Delete_<?php echo $cupcake1->DisplayIndex; ?>" /></td>
to:
<td class="eC_FormItem"><input type="checkbox" value="0" name="cupcake1_Delete_<?php echo $cupcake1->DisplayIndex; ?>" /></td>