Media organisation bugs in iTunes 9

Hi, has anyone noticed some bugs in the media organisation setting in iTunes 9?

For example; I set it up so that my media files are stored outside the iTunes Library Folder. Within Music I now have two folders: iTunes Media and iTunes Library.

Now when I download an app or an update for an app I already have, iTunes does NOT store it within Music/iTunes Media/Mobile Applications. Rather, it creates a folder at Music/iTunes Library/iTunes Media/Mobile Applications and stores the apps there.

This does not happen with any other kind of media.. movies and songs all go into the correct iTunes Media folder I set up.

Moreover.. now iTunes 9 refuses to remember my iTunes store password: even if I click on "Remember password" it just refuses to remember for the next purchase.

Any ideas on a fix?
is it me or is it a common bug?