Hi Eric
Sorry for the delay I thought I would do some investigating.
Essentially, you described the issue yourself – you are using another plugin called “show single variations” – this is kind of a hack into WooCommerce to break them out to appear as though they are their own products.
S&F, honors the WooCommerce way of doing things, and treats variations as part of the same product.
So what you have is 2 plugins modifying the query to do certain things.
Unfortunately we only offer complete compatibility for WooCommerce itself and not a plugin developed by some third party – although many will work, this one, modifying the query clashes with the modifications S&F makes on the main Woocommerce query.
Thanks