This issue may be caused by WooCommerce new version, it seems the product custom field (product designer) does not work with Ajax add to cart function, We will check and get back you soon with any update on this.
are you still looking at it?
In your previous Gecko 1.6.0 everything worked properly.
Even now if we roll back to 1.6.0 with the latest version of WooCommerce 3.1.2, Ajax add to cart function works properly.
So it seems that is not related with Custom Product Designer plugin.