Multiple Libraries and Music Folder Locations

I'm stumped.
I keep three libraries on my MacBook Pro. The folder structure for where the library and xml files live is basically:
~\Music\iTunes\ATV
~\Music\iTunes\Pete
~\Music\iTunes\Jen
Each library is associated with its own Music Folder, on an external hard drive, like so:
External\Contents\Main
External\Contents\PJP
External\Contents\JLP
I have iTunes manage the music files, keep things organized, and copy songs into the Music Folder.
When I open the "Pete" library, for example (by holding down Option when I click on iTunes in the Dock), it opens fine. I do what I need to do there, and quit iTunes. Now, somewhat suddenly, when I open the "Jen" library next (again by holding down Option while launching iTunes to select that library file), the location of the Music Folder in Preferences->Advanced has been changed to the location of the last library's Music Folder. In other words, the library should be pointing to \Contents\JLP, but instead is pointing to \Contents\PJP.
I can change the location of the Music Folder (a fairly long process), but the next time I open up a different library, the Music Folder location is similarly incorrect.
I imagine I'm just tired and overlooking a fairly easy fix/cause of this behavior, but it escapes me and I'll be grateful for your help.
Cheers.

I have noticed this happen when the computer temporarily loses a link to the external drive it reverts to the locally stored music folder but reverts to the external drive when it is available again. Don't know if a similar issue is what is happening here if so it may be something to do with the refresh rate at which your computer communicates with the external drive.

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