Unlike Joe Moose, I can see some valid reasons for having two or more pen names. First and foremost would be to separating two or more different types of stories you write. For instance, say you write a lot of Star Trek or Star Wars fan fiction you could use one pen name for those stories. You could use another pen name for stories that include incest as a major plot point. A third pen name could be used for coming-of-age or romance type stories.
Yes, using different pen names can lead to difficulties in the forum, but on the other hand, some individuals are likely to downvote all the stories by an author if that person seems agreeable with certain squirks, which multiple pen names used as described above would make it harder to do.