From my little experience with psyBNC I seem to remember there being a form of 'channel' that only users of the Psy can see, and I believe it was preceded with a ~ - with my little experience of Quakenet, I don't see the reason for the q~ to be mandatory? What does that mean? I have never had issues typing /join #channel on Quakenet. It could be that the q~ is 'fooling' PsyBNC and getting it mixed up.
If that is the case (which is purely an educated guess) then I can only think of using /join #channel as usual.