Blame the tsunami? From the RISKS Digest:

One of the two radio stations that emit Japan Standard Time signal stopped operating: the station is within 20 kilometers area (evacuation area) from the Fukushima Daiichi nuclear power plant.

Ever since the evacuation was announced, and the staff (2-4 people) left, the station stopped transmitting the signal. I suppose that the operator didn't want to possibly incorrect timing signal in the absence.

There are watches (including wrist watches) that can sync with the signal. CASIO, Seiko, Citizen and other makers of such clocks receive more than a dozen inquiries a day now. (I noticed something strange was going on with my watch that syncs at midnight, but that happens when the radio signal is not reachable due to indoor condition and didn't think much about it.)

The other station in the western part of Japan is in operation, but most heavily populated area, namely Tokyo and its surrounding area, is not covered well by the signal from that station.

Seismographs installed in mountain range and such uses the clock to sync the internal clock. The agency responsible for such instruments have resorted to use the wire signal for supplying the time information. Hmm, another risk of not so well tested software module and the somewhat unknown delay caused by wire transmission?