I am fairly certain I know what is going wrong. I have used Picard on my macbook pro, and I didnt get this issue. I believe this is due to how OSX handles file locations compared to Windows. OSX gives each file a global name to access it, so you can change the names and location while the file is open. But Windows does something different.
I just used Picard to find the names and metadata of about 30 songs from the same artist. It found all the right metadata, and saved it. When I went to go play the song in itunes, both to listen to it, and to have it update the info, it gave me a pop up that said "iTunes was unable to locate the file" and then gives me the option to browse to find it. Which I can do, but it requires me to manually do this for each song, and when I have 30,000 songs, it would be a pain in the ass.
Now what can I do to get itunes to automatically detect the song changes? Is there an option I need to have checked/unchecked, is there a script that will handle this for me, or will I simply have to go back to using OSX to do this?