Going to need more to go on, but first... Despite how they look, there's really very little different about XP and Vista, so stop being like the rest of the wannabe techs out there and using that as an excuse. If you don't know something, just say so. And this is more of a general shotgun type comment, not aimed specifically at you.
That being said, there are a great many things that could cause this, so you're going to need to go over there and start by making sure that there isn't a major virus or malware problem. You'll also have to try and play police detective, and figure out whether or not your friend is lying when they swear they didn't change a thing since you set the system up.
Make sure they didn't do something stupid like install some kind of registry cleaner/fixer/optimizer as well. Not so much because it's likely the cause of the files and directories going missing, but you're there, so you may as well try and take care of a few other things while you're at it.
But most likely, they did something to the computer, like running the restore media, and that's why the files and directories are missing. Just tell them that if they lie to you about something they did, it's only going to make it take longer for you to sort out what happened. I'm betting they'll have quite the story to tell once you break them down.
I'm really an xp person, but I helped a friend with a new laptop with vista move files from her old to new computer. I created a few folders on her desktop then used a jump drive to copy over the files.
A few days later she opened her computer and all the folders were gone, and we don't know where they are. I believe there may have been some short cuts I put on the desktop that are gone also.
Can anyone help us find these folders/files/shortcuts on her Vista laptop?