I know that the search does rotate. And that the stuff to show is rebuilt regularly. I also know that itch does not tell about how stuff works, to not encourage people to game the system. So do not expect to get an answer. But we can assume that there is a certain amount of rng involved.
And if near 100% of the traffic came from inside itch, a game might not actually be popular. Also in the other direction. If the only traffic comes from outside, but the internal links get ignored, it might be suspicious to the algorithm.
We do not even know how popularity gets weighted, do we? I very much doubt it would be a single number like page visits or download counter.
If they would not have some kind of running average, it would be always the same games on page 1 of browse. So maybe it really does randomly put games on bottom. If they recover naturally, they really are popular.
Of course it could also be some obscure side effect of how the browse index get's rebuilt, if a game get's a major update. Or some anti tampering methods. There do be people that try to fake downloads, ratings and popularity. It is hard to tell, if some game really gone viral, or someone bought clicks.
Or it might actually be very simple. If one does not use infinity scroll, the game in question is right on top of recent page two for tag fps. There have to be some trend setters for lack of a better word. People looking for recent games might be the start of some domino effect. Also, there is a 7 day option for popular games and the game in question is now 9 days old ;-) If the algorithm notices a certain lack of internal interest, it just might not be as popular anymore, according to its rules.
How do I put this. There are those celebrities that are famous for being famous. In my humble opinion, such a source of fame would not sit well with the philosophies of itch, what with the idea of giving all games a spot in the limelight of search results and such. Maybe they do something like that with popular browse.