server rankings are no longer based on average players? The servers are not ranked properly for the past week or so. What gives?

It is also possible the addition of settings for ranked servers, whatever it is. so not only refers to the average number of players...but also based on how long the player was playing on that server with a number of existing players.

Can you provide links to the GameTracker.com server pages of the servers with ranking errors?

While the average players value is a general indicator, it is not the determining factor. The ranking algorithm looks at activity over the past month, but more especially the recent time period (like the past week). The average players is just the mean number of players over the past month.

Why are there gaps in the server rankings? Several of the 30's, 40's, 50's are missing. You look at the list in order and numbers are missing. What causes that?

One of the servers may have been recently deleted, servers may have the same rank (if there are two servers at rank 26, the rank would be 26, 26, 28... it would skip "27"), or the server at that rank may be down currently.