I've noticed the Sense Clock widget sometimes trips up like that. Most of this might be a bit obvious, so sorry for that. Try turning off Autosync (circle with two arrows on power control widget) and turning it back on or also disabling and re-enabling gps to update your location.
Have you've checked HTC's weather settings. Click the weather image on the flip clock, go to menu > settings or hit the two circling arrows to resync.
I personally use the weather/flip clock just for the look and feel of it. The weather animations are certainly a win. For reliable weather information, I'm been pretty happy with WeatherBug Elite, it updates pretty frequently and pulls data from the station closest to you, as opposed to just using broad data from the same city.