boot.ini is a system file so if you have the folder options "hide protected operating system files (recommended)" ticked then you won't see it when you search. Also, there is another option for displaying "hidden files and folders" so if the settings say "do not show ..." then you might not see the file. The file itself should be one of the first ones you see under all the folders in your c: drive (not the Windoze folder).
I'm guessing you know all that, but you would not believe how many hair-pulling moments I've had because I hadn't set up someone else's machine to let me see everything.....