It seems that the "Submit AcoustIDs" button might be submitting ID's that aren't in the right hand pane and aren't associated with an album?  If so, I don't think that should be happening.

I just did a scan with an album where two of the tracks were matched to other albums.  Then I moved them to the album the rest of the tracks are in, and the fingerprint icons were then shown as red, that they would be submitted to this (different) album.

Then I moved one of them back to the center pane, out of the album so that it would not get submitted.  Then I submitted, and both fingerprint icons turned gray, which suggests it submitted both of them even though one was no longer associated with the album.

If I then moved the unassociated track back to the album in the right pane, it still had a gray (indicating known) fingerprint icon, even though it should not be known.