the most likely scenario is their voice mail boxes are pointing to exchange mailboxes that are different from the ones they are looking at with Outlook. There's no way to hide voice mails without some pretty fancy footwork at the client end - if they are being moved from the inbox by a rule then they wont be available to Unity over the phone so that wouldn't be the case either.
I'd take a hard look at which mailboxes they're pointing at for their subscribers and matching them up with the accounts they're pointing at from Outlook.