Songs I listen through Amua are very often not scobbled. I got this message on my personal page:
Some tracks you submitted have not been added to your profile for the following reason:
Spam protection triggered: You submitted a track dated earlier than your last submission.
Logged In: YES
user_id=1225650
Originator: NO
Do you use iScrobbler? If you are using iScrobbler or a similar program to scrobble your iTunes Music, try to quit that program (or turn off scrobbling) while using Amua. I have noticed that recent versions of iScrobbler try to scrobble your Amua tracks, which may cause the things you described.