Probably you have "invisible" folders, i.e. folders hidden to your Windows Explorer. Try changing the Folder options so that it will display also hidden files and directories, and system files.
You should see then these files and folders with a "ghosted" icon.
Look at their file attributes: you may see "hidden"...

Note that if some folders are marked with "system", the content you see in the Explorer may be distinct of what is really on the disk. "System" folders in Windows mean that their content list is accessible thorugh a special interface code that will enumerate or hide the inernal files (these files may be physically located elsewhere.) Some examples of such directories that are listed with a special "Browser helper" DLL are the Internet Explorer cache directories (Temporary Internet Files), and the user's "Application Settings", and "Local Settings" in which your temp folder is typically stored.

If you share all your user's home directory, in fact you are sharing the actual content of these hidden folders too, not necessarily the files that the Windows Explorer lets you see.

Some virus or spamwares are known to remap some folders using their own "browser helper DLLs", so that you won't see where they store the data they collect on you and cache locally. Most anti-spamwares tools will detect and help remove these undesirable "helpers" that monitor your usage on the local PC, even when you are not connected on the Internet.

Virii do the same by masquerading some Explorer DLLs that are copied into a new hidden system folder, and they sometimes masquerade the identity of the system DLL they have replaced, to show their normal name, size and date or even their content; in fact the DLL was effectively replaced by the Explorer modified with these helpers will not let you see that.

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