Hi there,
I've just been trying to reproduce this on Vista and I'm afraid I cannot.
I started by launching the Filter, then iTunes and setting a playlist playing.
After confirming that the Filter had spotted iTunes correctly running I minimised iTunes and started browsing the web (shhh though :P).
The only popup I saw was when the track changed and the play reported notification popped up next to the systray.
Can you please confirm the version of iTunes you are running, and perhaps some more information on what is popping up - I'm assuming you mean the iTunes application?
If you do not want the track play report notifications you can turn them off using the Filter's preferences form.
Regards,
Westy