Yep, that would indicate a script setting then. You can either choose to use the clean mIRC from now on or you can go through all your script files in the other mIRC (if there aren't too many) and look for something the code which is causing it.
You can look at your script files in mIRC by pressing ALT+R - to change the script file go to View > script file - where 'script file' is the next script file you wish to look at. If you click on the 'Find Text' button you can search for words in that file - I suggest you look for "Input" in each file and or the word "Beep".
Best of luck!
Regards,
