Once you have a couple hundred files in your mirc folder, things can get lost. I suggest having a "reload file" in the File menu in remotes, so that the initialization commands can be run again.

http://www.mircscripts.org/comments.php?cid=2161 no offense to the built in mIRC editor but this thing takes care of reloading the file and has a lot of great features I use frequently. You can also use this to edit your scripts and if you have "monitor file changes" set in the mIRC editor mIRC will ask you if you would like to reload the file when it detects any changes to any scripts at which point it will give you an option to run initialization commands.