Using WordPress 3.9.1 and WooCommerce 2.1.11.
I am having a similar issue and could not find any recent solutions. When I try to use custom permalinks for my shop/products, and you click on a product, I get page not found error (it should open a new page with product details). When i set my permalinks to the default settings, the catalog/product pages work perfectly, but my site URLs have the crappy permalink [hxxp://mysite.com/?p=123] which looks horrible and is even worse for SEO.
Would love a fix on this! Thanks!