Have you tried a safe boot & tried to find them. Have you checked the properties of the Shared folder to see if anything is odd, such as viewing options or permissions, etc.

If you're using Vista, it does have some odd behaviors at times so I've heard. Such as relocating some files or folders. I vaguely remember it does such under various conditions. (becomes invisible or something like that.)

There's also the option of setting up a test account with full admin abilities to access all accounts, search via that account.