One of the itch.io developers thought it would be a great idea to mess around with how games are displayed in the middle of their biggest game jam. They are also listed via amount of ratings... which is a no-brainer, feedback loop. He really should have thought before implementing these changes.
In regards to popular, it is ranking gams in this jam by how popular they are vs the rest of the website... again meaning popular games will get more views, ratings, etc.