A bug in mIRC (I know for a fact versions 6.03-6.16) is that when you do a server /list, any channels starting with a double hash (##) are not shown. I originally thought this was an ircd problem, but a /debug showed to me that it was mIRC. For me as a network administrator, this is a security issuse that people have exploited to set up botnets on a double-hashed channel (i.e. ##Flood) which they use as a base channel where why control the bots to flood other channels.
I have set up a temporary fix in the ircd's configuration by not allowing channels that start with a double hash, but this needs to be fixed in mIRC

Works just fine for me (6.16, 98SE). Have you checked you don't have 'Hide non-text channels' checked in the Channels List dialog (Alt+L)?

Ah, thank you. Problem solved.