Does the ruling on my work in affiliate marketing for computer software change if the financial dealings between the software-producing companies and the intermediary website are impermissible, or does the ruling depend only on the permissibility of the financial dealings between me and the website?

There is no objection to the fees taken by the website from companies, based on the permissibility of the commission being a percentage of the price, and the permissibility of combining it with a fixed commission. It is not necessary to investigate the lawfulness of the website's funds, unless there is a strong presumption to the contrary. If forbidden transactions occur between companies and the website, this does not cause harm, as long as your transactions with the website are permissible. It is prescribed to cease dealing with this website if a permissible alternative is found.