Problem: One library two locations?

Hi all,

I have a 2010 Mac Pro and have always had my itunes library on a separate internal drive. Recently I noticed my boot drive had been filling up and discovered that mobile apps have started to be stored in the Mobile Applications folder in an identical itunes library folder on the boot drive.

I'm assuming at some point I did an itunes update and it switched over to the default file location, "Music" on the boot drive.

In the itunes preferences my itunes media folder location is still listed as the separate internal drive, not the boot drive. Newly imported music is still going to the designated location.

Please see the attached image. The top panel is from my boot drive, the second is the separate internal hard drive. There's some minor differences in the way the two are organized. For example, in the boot drive "Automatically Add to iTunes" is under "itunes Music", but in the selected location-- the separate internal drive-- "Automatically Add to itunes" is directly under "iTunes".(just an example of one of the small differences in the way the folders are organized)

Again, the bottom panel is my selected itunes folder location from the itunes preferences and where I've always stored my music. The top panel is from the "Music" folder on my boot drive— an iTunes folder that I don't remember creating and where my mobile apps are now going.

Any way to get this smoothed out?

Thanks very much in advance for any help anyone may have