[scudlee]

@Sesshoumaru: This is known and is one of the main differences between the anidb and tvdb scrapers. Each (named) season should be treated as a separate series in its own right.
So you'd have:
Boku wa Tomodachi ga Sukunai
|---Season 1, Episodes 1-12 + Specials (Season 0)
Boku wa Tomodachi ga Sukunai Next
|---Season 1, Episodes 1-12 + Specials (Season 0)
Boku wa Tomodachi ga Sukunai: Yaminabe wa Bishoujo ga Zannen na Nioi
|---Season 1, Episode 1
Boku wa Tomodachi ga Sukunai: Relay Shousetsu wa Ketsumatsu ga Hanpanai
|---Season 1, Episode 1
(The latter two could also be treated as movies with the movie scraper)


@fireba11: What custom regex(es) are you using? "Kiba - 13.avi" won't match any of the defaults.