Use password authentication on Freenode
Some IRC channels on Freenode impose an authentication prior to joining. I have only observed this on Freenode, but I might be applicable for other IRC networks.
Luckily the Freenode IRC daemon supports communicating password during the connection.
This can be specified like this in your ~/.irssi/config
{
address = "irc.freenode.net";
chatnet = "Freenode";
port = "6667";
autoconnect = "Yes";
password = "secretpassword";
},
According to the source listed below, you could also try with a longer delay for your NickServ authentication. I have not tried that out, please refer to the listed source.