I'm currently finding that while on-access scanning is activated and I launch iTunes, iTunes runs as though it is launching for its first time. When I close iTunes and relaunch it, it's forgotton all the changes I make.
Disabling antivirus and launching iTunes, making changes, closing and reopening the program it does remember the preferences.
I have my operating system on C: whereas iTunes, it's music and library files and folders are all on my J: drive.
While anti-virus is disabled I can link the program to operate from the library I have on J: and no matter how many times I open or close the program, or reboot the system iTunes remembers these settings.
However when I enable the antivirus it forces iTunes to create new files within the C: drive and use these, making iTunes launch as though it's just been installed each time.