Just having the popups.ini file may not mean that it's loaded or that it is unchanged. I'd go into mIRC and press Alt-R, then click the Popups tab. Make sure there is stuff there for all 5 sections... to check each section, use the View menu to select sections 1-5.
If there is, then it is possible that you managed to get some trojan or you typed a bad command (/write $decode(hfda89ds723) type of thing ... btw, I wouldn't type that as I have no idea what that decodes to... it was just random characters... probably is safe, but just don't type it.
). I think reloading is your best option.
If you want to save the logs, just go into your mIRC folder and copy the logs folder to your desktop. Then install mIRC to another folder and then copy the logs folder from your desktop to the new mIRC folder.
****Make sure everything works fine before you delete your old mIRC folder.****