Are you referring to the /flash command as described in the help file, or the Flashing setting, that's available by right clicking on the channel name in the Switchbar/Treebar?
If the first, then a script will probably be required, however, if the 2nd, the setting stays until you change it. This was tested and confirmed for channel departure, network disconnect and mIRC closure. In all cases, the Flashing option remained checked when rejoined the channel (after reconnecting/restarting mIRC as necessary).