It seems that PayPal's automated scanning method to generate these warnings doesn't account for a scenario where sales could be coming from a site that isn't running its own ecommerce software and isn't using PayPal's own purchase buttons.
Most ecommerce solutions are either a "licensed" software package that's installed on the seller's own server, or a fully "hosted" solution which also manages the seller's site (or at least their storefront/sales pages). In either case, the server running the ecommerce software is also running the sales site/page where buyers place their orders, so PayPal can usually determine if a seller's ecommerce solution supports the latest HTTPS/TLS standards by scanning the site where those sales originate.
However, E-junkie is a hybrid of those approaches, where the ecommerce software is centrally managed on our servers, yet most sellers use our service by pasting button codes into their own site, so in our case the site where sales originate is not also the server running the seller's ecommerce software. Thus, when PayPal's scanning routine checks our sellers' sites, they're looking in the wrong place to determine if the seller's ecommerce solution supports the latest HTTPS/TLS standards, which can then generate the irrelevant warnings you've been receiving.