Ok I did a stupid amount of research so I could better update the comic. Now I assume you are talking about when it's the by popular right? If not you can ignore what I'm typing. I would also like to mention when I read what I did I did observations to check if this was right.
The primary factor for popularity is page views. Since we all know sometimes we keep going back to a comic without subscribing, it's one of the big ways the algorithms seem to keep track of how well we are doing. You'll note in the FAQ they strongly recommend against updating more than once or twice a week. So what happens is it seems to check how many page views you've had over the course of the current month (possibly life time- this is where I'm not sure) and divides it (as PART of the equation) by how many updates you've had total. This means an artificial drop with each new updated until people realize you updated and go check it out. My evidence to support this is a large part of the formula my observations when we update. Before an update I'll be near the top of page 4 of sci fi. Once the update is live, I drop down to the bottom or even page five. I'm more likely to move to the prior page if I have two updated close together (filler or announcement) if it is towards the beginning of the month rather than the end.
So as an example, lets say someone has 100 subs and you have 50. 100 subs has had 4 updates and 100 page views and you had 2 updates and 100 page views. This means you have 50PV per update while they have 25PV per update. This would push you up the list and leave them behind you.
Hope this helps.
