For some reason in WinXP, mIRC won't wite to INI files used for settings. Although scripts save to INI files just fine. This is the code I'm using:

wset { writeini $mircdirSystem\set.ini settings $2 $3- }

Have you tried
wset { writeini $mircdirSystem\set.ini settings $1 $2- }

Make sure the files aren't set as "Read only" (Right click on the file > Properties). It happened to me once, I was changing my settings in files such as mIRC.ini, or updating my variables, and when I saved the files it came back just as if I didn't do anything. I never knew why they got the "Read Only" attribute, but they definately did...