If your access to your boss's mail is for checking when he's not there then it may be perceived as 'snooping' and you should not mention it. Equally though, if your boss is at a level where people know his secretary has email access, then the HR person was extremely stupid and should be shot.
If, however, you have access to his mail so that you check everything, then he must know you've seen it. I would raise it and see where it leads. After all, you know you have an NI rating, so be assertive but positive and see what it means for you in terms of your job and what type of training/support you will receive in the coming year to ensure there is not an NI next year.
Good luck and keep us informed.
Jackie, Peer Moderator
www.iqps.org
