It pays to poke around in your music folder from time to time to eliminate inconsistencies. Yesterday I had a look and found two folders for Jane's Addiction: "Jane's Addiction" and "Jane_s Addiction". I had a look in iTunes to confirm that there is one artist with that name.
Here's what I think happened. I ripped one CD with iTunes 4.1 and the other with 4.2. It seems that with 4.2, Apple changed the way the app names folders to make them more compatible with Windows. As far as I know, Windows is picky about certain characters in filenames, whereas Mac OS doesn't care unless it's a colon or slash. I've seen the use of the underscore in music folders on a PC in place of certain characters.
I didn't like there being two folders for the same artist in the music folder, so I selected all the songs from both albums and renamed the artist to "Janes Addiction". Then I renamed it again, this time with the apostrophe. When I looked in my music folder again, both albums had been combined into the artist folder "Jane_s Addiction".
I didn't want to risk confusing iTunes, so I didn't alter the folder structure directly.