Do you have any timers running or are you using a bouncer to connect to your networks?
mIRC periodically "does stuff" on each connection, so do timers and bnc's-- if all your connections were initiated at the same time, they will all "do stuff" at those periodic times, potentially causing significant delay if what they're doing is resource intensive. There have been previous reports that psyBNC caused periodic freezing when connected to multiple networks because of data intensive commands it periodically sent to servers.
