So the Weather will affect only one department & not any other Department's ?
No, but you may have the "Weather Priority" function enabled in your scanner! That means that every two seconds or so, the radio switches to monitoring for a SAME (I believe) tone that will then switch your scanner over to the emergency message that your local NWS weather radio station would then be transmitting.
The result is a "hiccup" that occurs in the transmissions of the LVPD you are listening to, but since the NWS station has not sent the tone out, you hear nothing, just that hiccup interrupting what you are trying to listen to.
It could also be (as another reply earlier mentioned) the regular Priority function is enabled, but on a blank or rarely used channel.