Sounds like a combination of issues here. The normal location for a song in iTunes is <Media Folder>\Music\<Artist>\<Album> however the \Music folder in there is optional. It wasn't used prior to iTunes 9. It can be turned on via File > Library > Organize Library > Rearrange Files. To turn it off you need to manually edit the hidden .iTunes Preferences.plist file in the media folder, changing the integer value from 1 to 0. It would seem that somehow that flag has been turned off on your system.
iTunes generally assumes that any meta data it knows about is correct, but using Get Info may force it to refresh its knowledge of the file properties. If you have the Keep media folder organized option enabled then this refresh may also cause iTunes to check that the file is where it is supposed to be according to its metadata. If it isn't then iTunes can move and/or rename it accordingly.
tt2