The details of the error  message(s) would be helpful.

Has your IT staff  checked the SMTP server  to see if the alerts  are
actually getting sent that far?

Also, what distinguishing characteristic(s) do the "non-alert" users
share (e.g. are they all in a separate domain)?

Here is the reply from my IT folks:

"1. SMTP server  does not receive alerts  from MOSS to send out to
users. It gets stuck before it somewhere.
2. Non-alert and alert  users are all the same. We only have one
domain and everyone is in one OU."

They also say they are no longer seeing those errors, but the alerts
still aren't working. It appears they aren't related after all.

Let me know if you can think of anything else...

Is it possible that the mail server  is rejecting some alert  messages
for some reason? Have any new rules, policies, service packs, etc. been
applied to it recently?

On the SharePoint side, what do these users have in common (as opposed to
the "alerted" users)? There has to be some common factor here, and if the
messages truly aren't making it out of SharePoint, then there has to be a
clue there.

What logs are the IT folks investigating? Is this just the server event
log, or have they actually checked the SharePoint logs for errors?

IT replied:

"Nothing was changed to the email server. There are no rules set up
on it."

"To my knowledge these users are all the same."

"Checked the server  event logs and Sharepoint logs. I don't see
anything anywhere."

Does this help? I'm about to walk over to their department to check
on the list of folks to see if I can find anything in common among
them.

A new development: I started  testing some other site  collections (we
have a portal  site collection, three others, and then the my sites).
I set up a new alert  in each location, and I received  the "a new
alert has been created" message for all of them (including the
portal). I then tested them, and only received alerts  for changes
made in the other site collections. The only SC where I didn't get
the alerts to "fire" to me was the portal SC (the one where we have
those two news  and events lists  where all staff  have alerts).

Hope this gets a little further along, as opposed to a little more
lost.

What is the custom  web part  that your consultant fxed supposed to do?

It is supposed to get copies of announcements in sites across 4 site
collections. An event handler was applied to announcements lists
throughout the site  collections, and when someone checks the box
to "copy to homepage," the announcement is copied to the homepage.
The custom  web part  displays items from this "rollup" list and is
also security trimmed based on the security of the original item. It
seems pretty complex. I don't fully understand how it was designed
and how everything works together.

FYI: We are still having the problem. We have our IT department, the
consultant who built the web  part, and Microsoft all involved. I'm
praying someone finds and fixes the problem  soon. It's been an
embarrassment and not a good way to introduce everyone to MOSS.