It's certainly puzzling! I have NIS 2009 running under XP Pro SP3 and previously had NIS 2008 with the add-on pack. I use Outlook Express for my mail client and IE7 is the version of IE on that installation.
More background: It's a multiboot machine with VISTA and Windows 7 Beta on it all in separate drives so they don't interfere but I only handle mail on the XP Pro SP3 installation so let's leave that aspect on one side.
This is a desktop that my wife and I use each having our own desktops and our own email accounts on RoadRunner.
We use Windows Fast User Switching so can log on and switch from one desktop to the other without logging out and without passwords. I mention this because under NIS 2008 the Norton AntiSpam Icon on the Outlook Express toolbar did not follow when you Fast User Switched; it appeared for the one who logged on initially but if the other wanted to use it the first had to log out and the second log on.
Nevertheless, the AntiSpam identifying and sorting to the Spam Folder worked for both even if the icon was not there. You could right mouse click on a message and change its status to and from spam but not with the toolbar.
When I upgraded to NIS 2009 perhaps because antispam was integrated this problem disappeared.
So for me at present all I can say is that I don't have the problem the two of you describe.
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Since you both have switched between NIS 2008 & NIS 2009 -- and for one of you 2007 > 2008 > 2009 and for the other 2009 > 2008 -- without affecting the problem and given the total difference in the engines and behavior of the two versions I would suggest that it is best to assume for the moment that the cause is not in NIS. I don't suggest that to avoid it being Symantec's problem but because it seems more logical.
If we assume that for the time being, then the questions that arise would involve the mail client used:
-- plhermette refers to outlook; you don't say; are you both using Outlook or Outlook Express?
-- and whether Microsoft changed anything
and/or whether some external security change occurred?
Also whether your user/desktop/switching is similar to mine or not?
Can you both fill in the gaps on the various questions so we can see if we can get anywhere that way?