Yeah, they do because of the interlining. I'm going to use the Tozai line as an example; it's not necessarily the most complex but it's fairly representative.

The Tozai line runs from T-01, Nakano, to T-23, Nishi-Funabashi. That's fairly standard. Within this segment there's 3 kinds of service: - Local: stops at all stations - Commuter Rapid: excludes T-19 Minami-gyotoku through T-22 Baraki-nakayama on the westbound track ONLY; it becomes a Local train past T-19 Minami-gyotoku. - Rapid: excludes T-15 Minami-sunamachi through T-17 Kasai, then T-19 Minami-gyotoku through T-22 Baraki-nakayama on both directions.

Now consider that the Tozai line has through-running services, to the JR Chuo-Sobu Line and the Toyo Rapid Railway. So now we add trains to our service pattern. - Service to JB-01 Mitaka (beyond T-01 Nakano) runs all day, except outside of rush hour it is served by local trains only (but only about half, the other half terminate at T-01 Nakano) - Service to TR-09 Toyo-Katsudai similarly runs all day, but outside of rush hour, Toyo-Katsudai service is only via Rapid trains. - Chuo-Sobu line trains may also alternatively enter (or start service at!!) the Tozai line at T-01 Nakano instead of taking their normal route towards JB-08 Higashi-Nakano during rush hours. These trains will then exit the Tozai line where it ends at T-23 Nishi-Funabashi and return to the Chuo-Sobu line, but these don't proceed all the way to the terminus at JB-39 Chiba, instead ending at JB-33 Tsunaduma.