In the early days of the internet, newbies were a temporary problem. Most users were university staff, students, and business people... and computer geeks, of course. New users might take some time to fit in to the internet culture, but they were intelligent and motivated to learn, and fit in they would. September was a time of some note, as a flood of college freshmen would get access to the internet for the first time, and Usenet and other services would be flooded with a bunch of people who didn't understand how to web, who ignored basic social expectations, and who tested out the limits of their new toy in annoying ways.
Then, in September of 1993, America Online began offering Usenet access to their customers. Usenet was flooded with newbies, and more newbies, and more newbies... While most of these new users adjusted to the community expectations or got tired and dropped out -- as users had since the dawn of time -- there were always more newbies coming in.
This was the Eternal September.
As the name indicates, the flood of newbies continues across the internet to this very day. Usenet, ironically, is now much less Septembery than most of the internet, being very much part of Web 1.0, and very much not Web 2.0. AOL (previously known as America Online) discontinued Usenet access in 2005, and pcmag.com declared it officially dead in 2008 (they were wrong, but still). While other forums, including 4chan, Something Awful, and FARK, have used the term to refer to their own newbie problems, for the most part the Eternal September is now so much a part of life that there is no need to label it, and the term is more and more an irrelevant in-group reference.