I don't know your exact problem, but maybe this will help you
troubleshoot:

Immediate alerts  are sent, by an (event handler?) to the owstimer.exe
service. You can see this job definition in Central Admin

Daily and Weekly alerts are sent during Indexing, and can be
enabled/disabled from Shared Services, Search Admin screen.

There is a known issue with MOSS alerts  and Exchange 2003. The alerts will come
in blank and they cannot be opened. There is a patch for Exchange that fixes
it.

I believe this is it, http://support.microsoft.com/kb/930807/en-us

I appeciate you passing along this kb article, but we've determined
that this will not help with our issues since the patch resolves
issues with Outlook 2007. We currently still use Outlook 2003.

I would still appreciate any input anyone else has on this subject.

We have found that alerts  are not being generated in some cases. We
thought we had done something wrong in our code, so one of our
programmers replicated the issue in a vanilla installation using
the "Document" content type.

He found alerts were not generated when a new document was checked in
and any one of these three conditions apply:

* `Require Check Out' setting is enabled on the library.
* There is a column/field that is mandatory (other than the
required `Name' column).
* Some code that does a check-in for a newly created document (such as
an event handler).

I think our next step will be to log a ticket with PSS.

We had similar issues before: we will get the alert created
notification email but not alerts  all the time.

The problem came from the scheduled event and event cache tables had
new records inserted every 20 seconds and we had more than 300K rows
in less than a month.

After I stopped this insertion, all alerts worked fine. So you may
want to check your content database for more information.

Please let me know if I can be more helpful.

You stated that you stopped the insertion into these tables. How did
you go about that? Is this recommended?

The insertion came from an error message had nothing to do with any
Sharepoint or database issues or operations. That's why I stopped it.
If it came from any of the servers as either back-end or front-end,
then it's a different issue.

However, if your hosting servers have some many errors, you may not
be able to use it regularly or at all.