This is a difficult one to handle because it's a very unique behavior to Notice in mIRC. At present, there is no means to tell mIRC not to display the ChanServ notices in every channel it's seen in.
There are a few script approaches you can take, however. 1) use Halting Default Text for On Notice messages that ChanServ sends to you. 2) send fake messages to yourself using /parseline that either a) makes ChanServ re/nick itself to ChanServ-, or b) makes ChanServ appear to /part the channels it is in. That way, you'll only get ChanServ notices in the Active window/channel, and not all of them. Or 3) use On Parseline to make ChanServ Notices appear to be ChanServ Messages, and they'll all funnel into a /query window instead. Or 3b) Use On Parseline to translate ChanServ Notices into ChanServ- Notices (different nickname to the one in all your channels).
At least I won lunch.
Good philosophy, see good in bad, I like!