Not sure what to suggest. Are there any event logs showing a problem with the Volume shadow copy service? The files that you mentioned (if they are the only ones that were not backed up) shouldnt matter, they are only temporary files anyway. But I know It would be good to find a reason and solution to why they were not backed up even with AOFO turned on.
Just thought, are those files still on the server? As they are temporary files, they could have been deleted when the backup was to taking place, so it would be unable to open the file, do you have prescan on or off? I cant remember what the error is if backup exec tries to backup a file that no longer exists, I have had that before, but cant remember if I was using AOFO with it.
Are you using AOFO on any other servers?
David