Ok, how about "this chick is a scripting noob" help.
Try the following:
1) Open mIRC
2) Copy the following into mIRC and press enter (in any window):
//copy -o $qt($+($nofile($mircexe),defaults\scripts\popups.ini)) $qt($+($mircdir,scripts\popups.ini))
3) A popup should appear saying "File 'popups.ini' has changed, reload from disk?" Click YES. (If this doesn't appear, just go to the next step.)
4) Now copy the following into mIRC and press enter (again, in any window):
//load -ps popups.ini | load -pc popups.ini | load -pq popups.ini | load -pn popups.ini | load -pm popups.ini
Does this fix your problem?