Can't really think why that should happen if the tick-box isn't ticked.
That .js file will probably be partially named after the page on which the editor instance was that you edited. (i.e - if it was on a page called updatethis.php, then the .js will be called something like 'updatethis_somethingValue.js'.
The only other thing I can think of is that if rour iRite folder was inside another directory in your root directory, then if it has been edited, it will have created a whole new set of iRite (or HTMLEditor) folders in the root directory. It might be worth checking in there too, if that is the case.