I have a very strange problem that is preventing me from accessing a few files/folders.
This problem has occurred twice, and was caused both times by using the auto shutdown feature of a bit torrent client. Also, it wasn't the same client that was used each time.
Upon completion of the download the computer shuts down as normal, but the files (that were downloading) are now inaccessible in windows. Any attempt view them with the explorer, or an open dialouge box results in an error that crashes explorer.exe.
They cannot be viewed or deleted. They cannot even be deleted with the command prompt.
Check disk was run, and upon the first iteration it reported "deleting an index entry of index $0 of file 25" but it did not correct the problem. Subsequent iterations do nothing for it, and it finds no errors. Scan disk doesn't do anything either.
Bascally any invocation of the data contained in the folders causes this crash. For instance in explorer, all you need to do is hover the mouse over the folder containing the corrupted folder/files and it dies.
This strangest problem with all of this is the fact that the files/folders read and work perfectly in any cd-bootable version of Linux ie. knoppix, so I know the data is intact.
I have tried moving the bad folder to another location, though it still stays bad, now i can view the old location in win xp(without the folder there).
I have the suspicion that there is some meta data/file system data that is not viewable that is not organized properly for windows but Linux ignores. Is there at least some type of editor that will allow me to view this or at the worst, some Linux utility that will allow me to view the files and save them to new clean locations. They are only large wave files and could be easily readable in hex if necessary.
Oh, and the first time this occurred, I just deleted the files, but I'd rather not have to re download anything this large.

It sounds like a windows based virus. Have you run a virus check on the files? Maybe even try an online virus scan from another virus checker!