Surly the channels directory should only be created when you use /list and it doesn't exist?
Why does mIRC insist at creating this pre-startup.
To remove it automatically I am using:
on *:start: .rmdir channels
But this is less than ideal.
Another thing I have noticed is that if the directory doesn't exist, and you issue /list, the /list command doesn't attempt to recreate it, neither does it output the list to a file.