Folders and Files in Libraries

After upgrading from Vista Ultimate to Windows 7 Ultimate, I find that all of my folders that were in folders automatically included in the various Libraries (e.g. Document and Pictures) are now empty and files that were not in sub-directories are missing. In Vista and still in Win7 I have two drives (C: the system drive and D: the data drive). My Documents and My Pictures folders were and still are on the D: drive. Other folders and files on the D: drive are intact. It is just the ones associated with Libraries that are the problem.

I don't think the files are really missing since the amount of used space on the D: drive has remained the same.

Any idea of what is happening and how to fix it?

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