Multiple Library Confusion
I've just posted a brief article explaining how your system can get confused when using iTunes' multiple library feature:
Some of my AppleScripts for iTunes use a routine which reads the iApps.plist in order to obtain the location of the current iTunes library's XML file in order to get information from it. I occasionally get reports that these scripts don't seem to be working correctly; that the information seems to be wrong or doesn't correlate with track tags in iTunes. When the Correspondent and I investigate this phenomenon, very often it is because the iApps.plist contains the wrong location for the current iTunes library....read more here.