I haven't used the windows version in a while, but are the Auto Import directory settings per library?
Yes. Per Library. This works now. You can set up the Auto-Import fully, and it works when you choose Run Auto-Import Now, but it doesn't actually yet actually "monitor" the file locations.
If you ever do funky things with your Library files, read this (otherwise, ignore it):
Make sure you don't try to clone Libraries from outside the application, though, as this messes the system up (and confused me a while back). If you need to create a duplicate of an existing Library, you need to do it from within MC using the Clone Library function in the Library Management part of the Tree under Playing Now. If, instead, you copy and paste the library folder contents themselves to a new location, and then add that new Library, they get added with the same GUID and it messes up the Auto-Import settings (they switch together).