My wishlist was not working because my theme did not use any quantity fields on the product page. Adding this simple code (in product.tpl, right product column) fixed it for me:
<input type="text" name="qty" id="quantity_wanted" class="text" value="{if isset($quantityBackup)}{$quantityBackup|intval}{else}{if $product->minimal_quantity > 1}{$product->minimal_quantity}{else}1{/if}{/if}" />
