See where there's a similar problem with psyBNC caused by having the primary network be a network which supports CPRIVMSG and the others don't.

Note that this script works by deceiving mIRC into thinking that none of your networks support CPRIVMSG. I don't know if it would work to have this feature disabled only at some networks by inserting a line into the event handler, which would look something like:

if ($network !isin freenode) return