Library File Structure Problem

I have 3 partitions setup on my computer, one running OSX, one for WinXP and another FAT32 partition I use to store data which is used by both operating systems. I recently copied my music library to this partition and set iTunes to use this partition (and subsequent sub-folder) as the primary location for my music library. While I am now able to enjoy my music library in OSX and WinXP I encountered a few problems.
1)The file structure for itunes with album art, separate folders for music, film, podcasts etc... did not transfer from it's original location in "My Documents\My Music" to the new location. As a result, whenever I download anything like a podcast or video it gets placed in the music section in iTunes which makes organizing and effectively browsing my library difficult. I am tempted to simply copy the original files to my new partition and then manually reorganize it. However, I'm worried it will have no effect on itunes and new downloads will still get misfiled regardless of file type or worse, I might render the library completely unplayable.
2) While most of my music is accessible to both Windows and OSX, occasionally I go to play a song in OSX and recieve an error message saying that the file cannot be located. If I manually search for the file it has no problem playing it. However, once I switch back to windows I encounter the same problem there. If I don't locate the file in OSX, it plays perfectly in WinXP. I have not switched the location of the file or any other related directories. Presently, a number of my songs remain unplayable in OSX as to not disrupt Window's ability to access all of my music.
Any assistance in ironing out these kinks would be greatly appreciated, thanks.

Anybody have any suggestions?

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