One rule is not to enter ctcp commands in the Channel window. I've been using the status window instead.
But is there somewhere else I should be entering my commands?
I think what the room rule actually is, is not to CTCP the room, ex:
/ctcp #channel version
or
/ctcp #channel ping
they probably don't want their users to ping out from trying to reply
the commands within mIRC can be used in any window, as long as they're entered correctly; mIRC processes the / as a command, and does the command, rather than messaging the room.
(NOTE: not all mIRC scripts are set up for / as the prefixed command)