Find the option “Order by” – enables ordering products by Date, Post ID, Author, Title, Last modified date, Number of comments, Menu Order/Page order, Meta value, Meta value number, Matches same order you passed via the included parameter, Random order, Price;
Product by ID has the order of publishing date or order in the Product list. If you want to overite it, you should find this option and configure. You can set by date and change products publishing dates.
As for the second issue please provide the page URL and screen with the problem. What lightbox do you mean?