certain commands performed on-connect result in "unknown command" errors from the server, hence not being executed. e.g. "msg" results in such an error, while changing the "msg" to "privmsg" doesn't.
http://rafb.net/p/rh7aWV25.html
[01:22am] jane|mb: same prob
[01:23am] akempgen: ok :)
[01:23am] jane|mb: 421: msg Unknown command
[01:23am] jane|mb: weird
[01:23am] akempgen: good to know
[01:24am] • jane|mb tries one more time
[01:24am] jane|mb: works now
[01:24am] jane|mb: privmsg jane test
[01:24am] jane|mb: freenode-connect CTCP REQUEST VERSION
[01:24am] jane|mb: JOIN #colloquy
[01:24am] jane|mb: CTCP REPLY freenode-connect VERSION Colloquy 2.1 ...
[01:24am] jane|mb: 505: Private messages from unregistered users are currently blocked...
[01:25am] jane|mb: sorry for the flood :S
[01:25am] • jane eyes nightstalker
[01:25am] nightstalker: ?
[01:25am] nightstalker: what did you change?
[01:25am] jane: 'msg jane test' to 'privmsg jane test'
[01:26am] nightstalker: mkay
[01:26am] nightstalker: but thats not a fix :)
[01:26am] jane: i know