Ransom,
To get the help for /join you type /help /join -- it should bring you to the option of the two /join commands immediately.
More pertinant to the topic: the channel windows should not reactivate during a reconnection unless you have an ON CONNECT script or perform-on-connect setting that uses join without -n. You've already been told a working method to stop reactivation, this is the definitive answer. The fact that it doesn't work for you does not mean it does not work. Channel windows do not reactivate for me on a reconnection, so this is in fact possible in mIRC.
Third-party scripts are known to mess with standard mIRC behaviour, so if a script is the cause you'll either have to fix it (yourself) or disable it.
In mIRC type:
//echo -a $script(0) $dll(0) $md5($mircexe,2) $version $os
Report the results here.
