Trustee was your spam as severe as this?
I'm not clear myself how the notification system work if a URL is in the post but it is possible that if someone has had previously accepted posts the notification does not apply to them?
Notifications do not apply to certain roles. You may want to investigate the user accounts posting.
Reinstall Askimet and double check your key is active, it will warn you if it is not anyway I think.
Also is it possible that pinging services and settings have changed after upgrading.
I really don't think there is a fault in 3.2.1 causing this not in terms of a bug but I'm wondering if somehow the installation caused a change or corrected something that was previously fault maybe even disabled using customisations in the WordPress core? Had any work done to your WordPress, did you install it yourself?